The story begins with XANA-possessed William, unidentified, passed out face down on the shore of a beach somewhere in the Digital World. He is found and prodded by a concerned, unsuspecting Digimon. XANA-William then snatches the prodding limb of the unfortunate Good Samaritan before slowly and menacingly tilting his head upwards to show the pulsating Eye of XANA on his forehead with an inhuman growl. The Digimon is justifiably terrified. End opening scene.

Next, we're introduced to Odd Della Robbia in his bedroom, playfully chatting with Kiwi. From there, we get a general idea of who Odd is, where he attends school and that it's currently spring break, and the friends he'll be returning to when he returns to Kadic Academy. He's in one of his usual good moods until he tries to leave and discovers that his older sisters have barricaded him in as their idea of a practical joke. After a few attempts to break out or at least appease who whichever sister is outside at the time fail, he turns back in and finds Kiwi messing around with something he pulled out of Odd's bag. It's Odd's Digivice, but it's the first time he's seen it, so he doesn't know what it is. As he fiddles with it out of curiosity, it causes a Digi-Port to open on his computer. Again, he doesn't know what that is; both of these go unidentified as a result. More screwing around leads to Odd getting pulled through the Digi-Port and into the Digital World.

After a moment to collect himself, Odd realizes he now looks like his Digital Avatar that he normally appears as on Lyoko. This makes him realize that, while this is clearly not Lyoko, it's still some form of digital space. Before he can ponder it much further, a small creature pops into view and gets all excited to see Odd, even knowing his name. As they walk and talk, with the creature calling himself a Digimon named Bukamon and giving a basic rundown of what Digimon and the Digital World are, Odd spots a strange dome in the distance. The Digimon admits no one knows where these strange domes came from nor cares to get too close; they do get just close enough, however, that Odd can see the familiar-to-him Eye of XANA on the gate and realize who built these gates. Some of XANA's basic monsters march around the parameter, and Bukamon claims these strange robots won't attack unless given reason, right before they spot Odd and open fire. Responding to his partner's confusion, Odd casually explains that they're already acquainted and fires Laser Arrows, managing to destroy a few. Impressed, Bukamon decides to join in, stepping into the fray before channeling energy from his link to Odd through his Digivice and digivolving to Gumdramon. Working together, the two manage to defeat the remaining XANA monsters before deciding to high-tail it before reinforcements are sent. Once they're away, Odd nicknames his partner Gumbo and decides to give him a basic beginner's rundown of Lyoko and the fight against XANA, giving an abridged story of how they lost Lyoko and a new recruit named William but apparently, Lyoko's creator hiding in the Internet sent them an e-mail that'll really turn things around. The scene ends before he elaborates.

We next go to the factory and the lab, getting a quick description of these locations as we see Jeremy and Aelita (two friends Odd spoke of) working at the computer. Their discussion goes into their continued search for William and then the major undertaking of programming the data Franz Hopper sent in his e-mail. Whatever mystery project they're working on, it'll be ready by the time everyone's returned to school. After a quick time skip, the whole Team Lyoko meets in Jeremy's dorm room, where they discuss how Jeremy and Aelita's project from the e-mail should be ready that day and that XANA's in for a surprise. Odd takes the moment to show off his Digivice and then use it to open a Digi-Port on Jeremy's dorm computer and invite Gumbo to meet the gang. Most are astonished, but Jeremy (still no less intrigued) recognizes him to be a Digital Monster native to the Digital World (Gumbo clarifies that they say Digimon for short), as Franz Hopper mentioned concepts such as this in his video diary. Jeremy asks to borrow Odd's Digivice so he can examine it. William is asked about, and Jeremy explains he gave Principal Delmas a cover story about William being overseas until they can find him somewhere in the Digital Sea. Gumbo balks at the body of water named, saying how it's the most dangerously turbulent corner of the Net Ocean with a bad reputation that anyone not equipped for deep-sea navigation would have their code ripped asunder just by falling in its currents. Jeremy acknowledges it's a long shot trying to find William in such an environment, but they have to at least try. They recall a story of how Yumi once fell into the Digital Sea, and by sheer luck they just happened to have a one-shot materialization program that could locate and bring her back.

There's a brief lunch break before the gang head to the factory; they have a brief run-in with Sissi and her two minions, after which Odd gives a quick explanation to a hidden Gumbo on who Sissi is. Over lunch, Odd confides to his friends that he showed Gumbo Paco, the King of Disco, an old video of the gym teacher Jim that he's supposed to keep secret. Odd's confident that telling his new little partner would be fine and that no one else will find out, but Sissi is eavesdropping. She doesn't pick up on what the "new little partner" talk is, but the Paco secret is all she needs to hear. Afterwards, once Team Lyoko is at the factory, Jeremy launches his big project at last: recreating the destroyed Lyoko. Or at the very least, the core sector of Lyoko; the surface sectors would have to be individually rebuilt one at a time. Odd, meanwhile, gives his new friend a quick tour of the lab and scanner room below; it's explained how the scanners preserve the Lyoko Warriors' bodies, bringing them back if they're fatally injured on Lyoko. Jeremy wants to work more on it to get the surface sectors done as soon as possible, but his friends convince him to get some shuteye first. After everyone has already left, one of the scanners activates for seemingly no reason. End part one of multi-parter first episode.

The next morning, Odd his horrified to discover that Sissi posted Paco, the King of Disco to the Kadic newspaper, and now Jim assumes he is to blame. While Odd is trying to do damage control, Ulrich visits Jeremy in his dorm to show that another Digivice like Odd's appeared near his bed. Another Digimon appears on Jeremy's computer screen when Ulrich activates it, identifying himself as Tsunomon and explaining that his Digi-Egg hatched inside some weird code-lined Tower, outside of which was some big, blue blocky room. Jeremy realizes in amazement that Tsunomon is within Sector Five, the core sector of Lyoko that he and Aelita had just finished recreating Tsunomon mentions he saw another Digi-Egg inside the tower as well. They go to find Odd to tell him, running into Yumi on the way, but they find him arguing with Sissi, who spots them and goes on to try and interrogate them about William's absence when a teenage boy they recognize as William himself shows up.

In private with William, they question him, but he says he only remembers being attacked by a creature called the Scyphozoa, and then his memory is completely blank up to when he woke up in the scanner room early that morning. The two Digimon are amazed, asking many questions, which causes William apparent confusion for multiple reasons. That evening, Jeremy has returned to the factory to continue working on the next sector and study Odd and Ulrich's Digivices with a new port he rigged into the supercomputer keyboard. While Jim is forcing Odd to memorize the entire Paco video and recreate the dance moves himself as punishment for allegedly breaking his promise, Aelita is visited at her dorm by William, who advances on her while revealing he's still under XANA's control. At the factory, Jeremy sees William arrive in the lab and starts to talk about some of the amazing things he's learned by studying the Digivices, but he trails off when he sees Aelita unconscious in the elevator and then gets a better look at William, realizing the truth too late as XANA-William incapacitates him with an electric shock and throws him out of the chair. XANA-William runs a self-virtualization program, and both he and his kidnapping victim are already in Sector Five by the time Jeremy comes to and gets back to the computer.

Jeremy calls Ulrich immediately, informing him of the situation that, despite the only Tower on Sector Five not being active, William is still possessed by XANA and has taken Aelita to the reconstructed Sector Five. As Jeremy calls Yumi, Ulrich calls Odd. But Odd is still at Jim's mercy, and Gumbo is trying to figure out how to get him out without getting caught. He spies a small group of students gushing about Paco and sneaks over to act as a voice in the crowd and manipulate them into going to the gymnasium to shower Jim with praises. Odd escapes, catches Gumbo watching from around the door, and deduces that he's the one who got him out. Ulrich makes it to the factory first and is virtualized, but not before Jeremy returns his Digivice to him, saying he's "gonna need it." In the Sector Five arena, Ulrich asks about the key mechanism they used to trigger to cancel a countdown, which Jeremy informs him that he and Aelita removed it when rebuilding the sector.

Aelita, meanwhile, has managed to momentarily evade her captor and runs off into the maze that is the Core Zone. Tsunomon comes hopping through and sees William advancing on the terrified Aelita. He bravely tries to intervene but is punted like an American football, which just makes him mad. Ulrich arrives at the scene just as Tsunomon is attempting another round, and his immediate concern plus having the Digivice on him causes Tsunomon to digivolve to Elecmon. The upgrade gives him more of a fighting chance, but Ulrich still needs to step in to make it more of an even match. Yumi arrives in the arena around this time and gets the same spiel about the removed countdown and key. Ulrich and Elecmon manage to give William some legitimate trouble together, but William manages to blow them away (Elecmon is knocked unconscious, and Ulrich is devirtualized) and recapture Aelita before she manages to run off. He traverses the Core Zone towards the exit to the Celestial Dome, with Yumi racing through to try to catch up.

Around this time, Odd and Gumbo arrive, having caught the gist of what's happening in Ulrich's voice mails. Jeremy hands Odd back his Digivice and says it can let the two safely travel through the scanner to Lyoko together, but he won't elaborate on why on account of time being of the essence. Odd hurries off to the scanner room and is virtualized to Lyoko with Gumbo, is given a rushed shorthand version of the ditched key and countdown spiel when he starts to ask, and they race off towards the Celestial Dome. He catches up to Yumi just as the Overboard and Overwing are materialized at the bridge, and both mount their respective vehicles with Gumbo tagging along; William is already flying around the open space of the Celestial Dome on a black Manta with Aelita. Just as everyone is wondering what William is there to accomplish, the bridge out of Sector Five into the empty space where Sector Two would be opens up. Since there's nothing but Digital Sea outside of Sector Five, Jeremy realizes William is going to try to throw Aelita down into the Digital Sea, which Gumbo points out obviously would be bad. Outside of Sector Five, William manages to take Yumi out of commission, but Odd manages to destroy his Manta ride while he's distracted and then swoop down to catch Aelita in time. Foiled, William retreats into the Digital Sea.

The following evening, Team Lyoko (now also consisting of Gumbo and Elecmon, whom Odd has dubbed Leon) meet in the factory lab to discuss William's recent return and his apparent goal to throw Aelita into the Digital Sea while Jeremy is starting work on rebuilding the first surface sector: the Ice Sector. They also discuss the Digimon and the things Jeremy learned while examining Odd and Ulrich's Digivices. He lays out a detailed explanation of how the Digimon take physical form in the real world that's basically summarized as that they're fundamentally the same as XANA's polymorphic spectres, advanced versions of his spectres that can take solid form. The Digivice binds the human and Digimon partners' code together, allowing the Digimon to borrow energy from the human to help sustain its polymorphic form as well as "digivolve" to higher levels, but it also allows the scanners to distinguish between the two sets of codes when both enter a single scanner and transfers both separately across the material-digital barrier during the virtualization process.

The team declares their ongoing plans to try bringing William back, figure out why XANA wants Aelita dropped in the Digital Sea, and come up with a means of traversing past the Digital Sea to the rest of the Digital World to try determining XANA's plans beyond Lyoko. Meanwhile, there's supposedly going to be a live performance of Paco by Jim due to popular demand, and most of the others set off back to school in order to catch it. Jeremy assures them he'll catch up once he's finished a bit of coding on the Ice Sector's pending return, but shortly after they leave, he's surprised to find another Digivice sitting on the back of the interface keyboard. When he notes aloud that it's clearly neither Odd's nor Ulrich's, a voice from the computer tells Jeremy that it's his. He looks up to see an open window with a kappa-looking creature smiling back at him. End of multi-parter first episode.

At the start of the next episode, it's been a few days, and Yumi is with the others in Jeremy's dorm describing how she discovered another Digivice like the three others already found among her things and, after shooing her little brother away, opened a port on her computer and found the critter known as Tanemon. Tanemon, upon being addressed, is shown to be on Jeremy's bed alongside Gumbo, Leon, and the Digimon who claimed partnership with Jeremy, Chapmon. Aelita is entertaining the Digimon with a mixtape she made months ago when she first learned she had a talent for DJing. Jeremy is shown to be a bit on the irritable side, as he's been forgoing sleep those past few days working on the forging of a new and better Ice Sector and working to upgrade his friends' weapons, Avatars, and powers.

The Chapmon is shown to be visibly concerned by this, and he offers to try helping with the workload to ease his partner's burdens, an offer he's apparently made a few times already in the time between episodes. Jeremy is uncertain this new ally can quite follow with the complex coding procedures involved in what he does, but Chapmon surprises him by casually going over some of those procedures out loud and saying he'd been closely watching what he'd been doing and learning in his observations. He also claims he knows a thing or two about code, as he'd expressed interest in being a nurse in his previous life, something that would require an understanding of code when looking after beings made of it.

The school takes notice of William's sudden reappearance and then just as sudden disappearance, but Principal Delmas receives a call from William's father claiming that he is sick with a fever and needed to be pulled back out of school. The call is actually a deep-fake from Jeremy to buy himself some more time. Unfortunately, the real James Dunbar also calls, leaving Principal Delmas confused as to who's real and who's fake. Jeremy's been at the factory lab, explaining aspects of Lyoko to his Digimon partner before finally completing and launching the recreation of the Ice Sector; Chapmon watches on impressed. As he continues to work, Ulrich calls to remind him he's on thin ice when it comes to gym class and can't afford to skip another one. Jeremy, pondering to himself how he can be in two places at once, mulls it over before looking at Chapmon and coming up with the idea of making a polymorphic spectre of himself, something Chapmon is surprised he can do. Jeremy is confident he can do just that using previous brain scans and activating a Tower to bring it to life, but Chapmon points out that activating Towers is primarily a XANA thing and wonders if that would be an issue. Jeremy assures him he's learned from past experiences and knows how to protect his Towers from XANA. He then gets to work creating the polymorphic spectre program and activating the Tower to run it. A Jeremy clone is created in the lab, and Jeremy tells his clone to go cover for him at gym. The clone makes some uncharacteristic finger-gun gestures and confidently struts from the factory, but Jeremy thinks it's probably nothing.

After Jeremy spends some time chatting with Chapmon about the Tower system, he realizes he should probably check in on his clone at school. He rings Yumi up on video call, getting a couple of annoyed friends calling him out for pulling the clone stunt without warning like that and word from Yumi that said clone is the biggest flirt she's ever seen; she points the camera of her phone at the clone to show him making flirtatious gestures. Chapmon (half rhetorically, half genuinely) asks if that's probably nothing, and Jeremy admits otherwise, calling it "an emerging quality that appeared unexpectedly." After their phone call ends, in which the others agree to keep an eye on the clone at gym class, Jeremy returns to his conversation with Chapmon, explaining more about the Towers as the Digimon listens with complete interest. Jeremy's about to talk about something very cool he was able to do with some of the data Franz Hopper e-mailed him when an alert from the supercomputer cuts him short. On Lyoko, William is trying to force XANA's will onto Jeremy's Tower. Jeremy gives the others a quick warning over the phone and assures both them and Chapmon that he can counter XANA's hijacking attempts by rerouting energy from Sector Five.

Jeremy talks with Chapmon a bit about William, about how he'd been a source of frustration at times but a valuable asset at others, and how they ultimately chose to bring him into the group when the frequency of XANA's attacks started taking a toll on everyone's personal lives, only for XANA to take advantage of his inexperience and possess him. Around this time, William is gathering more of XANA's energy for round two with Jeremy's Tower, but Jeremy quickly counters with some more of Sector Five's energy. After that crisis is momentarily averted, Chapmon offers to watch over the Tower some time so Jeremy can catch a break, and Jeremy resigns to the fact that the Digimon isn't giving up on that. With some prodding, Jeremy admits to Chapmon that he just wants to do everything he can to protect his first real friend group and that he's scared of what XANA could do to them if they don't stay on their toes. Chapmon just replies that clearly, Jeremy's friends care about him just as much as he does about them and worry seeing him close himself off for such long periods of time, at times without food or sleep. "You don't have to do this all on your own. Teach me what you can, and let me help you, partner." This sentiment finally breaks through to Jeremy, but he playfully teases that Chapmon probably can't do much typing with those flippers; he just laughs it off, saying he'll digivolve into something with more digits.

Shortly after, Ulrich calls to say that he, the girls, Leon, and the Tanemon who appeared to Yumi have arrived at the factory to help with the Tower situation while Odd and Gumbo are holding the Jeremy clone back at the school. Jeremy has run out of Sector Five energy to protect his Tower, so he sends the arrivals to Lyoko to handle it while the two who remained deal with the now XANA-controlled clone. On Lyoko, the human Lyoko Warriors take a moment to check out their updated Avatars before going to confront William and a squad of Tarantulas at the Tower, located deep down in the edge of the Ice Sector on an iceberg. As the fight breaks out, Yumi and William engage, and William managing to get in a hit and knock Yumi down prompts her Tanemon to jump in to her aid and digivolve into Floramon. Ulrich and Leon tackle a pair of Tarantulas while another pair leap to the iceberg to guard the now red Tower. They fire at Aelita's feet as she tries to slide down the path towards the iceberg, causing her to slip and fall towards the Digital Sea, but she inadvertently activates a bracelet on her right hand as she falls and activates a pair of angel wings. Jeremy programmed those for her as a surprise; some cute flirting between the two occurs, getting a grin from Chapmon on Earth. However, the Tarantulas still standing guard make it near-impossible to try flying in, so they have to be dealt with first.

Yumi and her Floramon partner move to go try and help Aelita get past the anti-air defense, and Ulrich moves to distract William with a Triplicate; this is only a momentarily stall, as William quickly deduces which of the three is the real Ulrich and devirtualizes him with a quick stomach stab. William ignores Leon to run after Yumi and the Floramon, leaving Leon to chase after indignantly. While the Tarantulas have their attention squarely on Aelita, who's dodging all of their laser fire, Yumi and her partner manage to get the jump on and destroy one. But the other manages to strike at the Floramon, knocking her over the edge of the iceberg, and Aelita swoops in to save her before she hits the Digital Sea below. This causes her to get struck by laser fire as she deposits the Floramon back onto the iceberg, and her wings are damaged, leading her to falling backwards towards the sea, herself. This is witnessed by the approaching William and Leon, the latter panicking and throwing a Lightning Knife Strike at the falling girl, which devirtualizes her just before she hits the water.

Meanwhile, on Earth, Odd has called Jeremy to inform him that the Jeremy clone has run off on him, and Jeremy responds by locking the lab door to keep him out. The clone eventually manages to break through the door, but Odd and Gumbo were given enough time to arrive through an alternate passage past the factory boiler room and tackle the clone. They fight, but "Jeremy 2" manages to throw both aside and advances on Jeremy. Chapmon tackles out of desperation, and the Jeremy clone attempts to shake him by electrocuting him. To everyone's surprise, including the Chapmon's own, Chapmon absorbs the energy from the fellow polymorphic spectre which, combined with his desire to protect Jeremy, causes him to digivolve into Kamemon. This motivates Odd's partner to rejoin the fray alongside Jeremy's, and the two working together just barely manage to hold their own against the enemy digital being. Ulrich looks after Odd. This is around when Aelita arrives in the lab after having been devirtualized on Lyoko. While the Digimon are holding the Jeremy clone back, she takes this opportunity to hop on the interface and check in on Yumi.

No one on Lyoko was particularly happy to see Aelita devirtualized, the heroes for the fact that there was still an activated Tower and William for the fact that he still wanted to knock her into the Digital Sea for still unknown reasons. However, he quickly turns his gaze to Yumi on the iceberg and, when Leon tries to intervene, sends a slash at the Elecmon that gravely injures him and takes him out of the fight. He then leaps to the iceberg where the Tower is and shoves Yumi over, but not before Yumi grabs him and manages to pull him with her. Her Floramon partner manages to catch her with a "rope" move and pull her up, and William falls alone into the sea. Aelita calls in by the time Yumi has her footing and tells her that she'll have to deactivate the Tower, which confuses Yumi as Aelita's supposed to be the only one who can do it. Aelita just says that she and Jeremy will explain later, but Yumi has to get to the Tower as the Digimon fighting Jeremy's clone can't hold him back much longer. She walks Yumi through the process, and the tower is deactivated just before the clone can attack her after having broken past the last line of defense. Now safe, Aelita tells the Floramon to carry Leon into the Tower as well, as a minute or so there will restore his Life Points and heal his wounds.

Once everyone's back on Earth, Jeremy explains what he admits he probably should've earlier, and it's also what he was trying to tell Chapmon (whose "rebirth" into Kamemon by "lightning" is compared by Odd to the creature of Mary Shelley's novel, earning him the nickname Shelley): Among the data Franz Hopper had e-mailed him was the raw code for the Annex Program that allows Aelita to access Tower programming and deactivate them; he was able to apply that same code to the Avatars of the other Lyoko Warriors when upgrading them. Since Aelita no longer necessarily needs the other Warriors to fight for her, he figured it was about time they don't necessarily need her to deactivate the Towers for them. Now it's just a matter of fighting together to get to the activated Tower, and whoever reaches it first deactivates it. Odd quickly challenges Ulrich in a race to the activated Tower next time there is one, and he gladly accepts. The team realizes that damage has been done on school grounds that can't easily be explained away, which Gumbo realizes means they're "gonna do that time travel thing". Jeremy affirms this and turns to whisper some instructions in Shelley's ear; the latter hops into the computer chair and starts typing in a command. Jeremy says his iconic, "Return to the Past, now," and the jump back in time he just taught Shelley to program goes off.

Jeremy attends gym this time around and admits to the others that Shelley wore him down and got him to code an interface for him in the Sector Five Tower, allowing him to pitch in with ongoing projects like the recreation of the other sectors when Jeremy has to step away. The team then wonders what to do about William until they can figure out how to free him, since the school is starting to get suspicious; Gumbo says he knows a guy. He come back from the Digital World some time later, bringing with him a Renamon he claims he helped out of a jam at some point while waiting for Odd to show up. Renamon agrees to shapeshift into and take William's place at school, provided everyone provide as much info on the guy as they can for a convincing act, partially to repay the Gumdramon but mainly out of boredom.

Opening the next episode, Jeremy is in his dorm, talking to Shelley on Lyoko as they're nearing completion of the Desert Sector. In this time, they also discuss possible ways to travel beyond Lyoko to the rest of the Digital World, Jeremy pointing out that even when they do finish recreating all of Lyoko, they still won't have an easy means to safely leave the Virtual Shell containing Lyoko and travel the treacherous Digital Sea waters. They can use their D-3 model Digivices to open ports from virtually any web-enabled computer, but they'd lack the supercomputer's resources and the safety net of the scanners if they lose all their Life Points. Shelley remarks how his type family, the Deep Savers, are best suited for aquatic travel, but even lesser Deep Savers like himself are ill-equipped to handle the Digital Sea. He says their best best would probably be if they can hitch a ride in, say, a Whamon. Or a submarine, Jeremy chimes in enthusiastically when the idea hits.

Meanwhile, Yumi arrives at the gymnasium, where she joins Ulrich and Odd at the bleachers. Leon and Gumbo are hiding under said bleachers as Yumi's Floramon joins them; when Leon addresses her to tell her she's "missed the show," Yumi's partner corrects him to say she goes by Florence after hearing Odd talk about the Italian city. In the center of the room, Aelita can be seen shaking hands with a platinum-blond haired man standing next to a proud looking Jim. Florence asks who the man is, and Leon identifies him as Chris Morales, Jim's nephew and the drummer for the Subdigitals, which Florence recognizes as the name of that rock band Yumi has been playing music from for her. Gumbo says that Chris was there auditioning young DJs for the chance to open for one of their concerts, and it's looking like Aelita just secured herself a spot. After Aelita waves goodbye to Chris as he and his uncle leave, she happily sprints to her friends as they voice their congratulations.

They meet back at Jeremy's dorm, where Ulrich discusses how the band used to be called the Subsonics until some legal dispute in Canada prompted the record company to force a name change. Ulrich claims he likes the old name better with Leon chiming he prefers the new one, which Ulrich teases is probably because Leon's got digi-bias. They all chatter about things like the band members, including lead singer and guitarist Nico and bassist Ben, and their songs like "Planet Net", "Angel of Mine", and "Break Away". Jeremy offers his own heartfelt congrats to Aelita for making the cut before asking her if she'd have time between schoolwork and DJ practice to help him and Shelley work on their digital submarine project; Shelley humorously chiming in that he offered to check in with some old friends from Factorial Town to see if they have an old one they could acquire, but Jeremy said they can build their own. When asked about the sudden interest in building a sub, Jeremy explains his concerns about the mystery dome Odd and Gumbo saw with the Eye of XANA on its gate, as well as the fact that others like it have supposedly been found around other points of the Digital World.

Jeremy explains for the benefit of the Digimon how Lyoko and XANA were created by Aelita's father, Franz Hopper, but then XANA turned against Hopper and tried to steal certain key files on the virtual landscape from Aelita. Late last year, XANA finally succeeded in draining Aelita's mind in order to acquire those "keys" and escaped the confines of the supercomputer into the Digital World. Aelita was alive today, because Hopper sacrificed a great deal of his energy to restore her memories and breathe life back into Lyoko before disappearing, and they hadn't heard from him again until after William had been possessed and destroyed the core data holding Lyoko together, at which point he e-mailed them from hiding with the instructions on how to recreate Lyoko. Instructions they were still in the process of following. Jeremy says that Lyoko is surrounded by a "Virtual Shell" that protects it from the Digital Sea currents and masks it from unwanted detection, and the "domes" that have been appearing somewhat match the description of the shell. This leads Jeremy to deduce that XANA has used the key files he stole from Aelita to erect other virtual landscapes in other places of the Digital World, supported by other supercomputers elsewhere in the real world to spread his influence.

Around this point, Shelley happily informs Jeremy and the others that he's finished his part on their "desert-scaping" work, and Jeremy tells him to upload his share of the data to the factory interface before asking the group if they're ready to go welcome back another piece of Lyoko. The group heads to the factory, where Jeremy launches the program and initiates the recreation of the Desert Sector. After a quick cheer, they virtualize to the Desert Sector to check it out, and the next bit of story goes over the Lyoko Warriors checking out this new Desert 2.0, which includes the occasional cactus clusters in a few different species courtesy of digi-seeds acquired by Shelley. They stop for lunch, and the humans go to the cafeteria to talk about things like the fact that they're already over halfway done rebuilding Lyoko now, so they'll be done in no time at this rate so they can then focus on creating their vehicle for traveling beyond. After Aelita finishes, she leaves to pick up her demo CD from the gym, where she just remembered she left it after her audition with Chris.

After she gets there and picks the CD up, Shelley slips in to tell Aelita that XANA has activated a Tower in the recreated Desert Sector but Jeremy can't reach her phone for some reason. She suggests calling him from her end, but Shelley insists there's no time and rushes her along, causing her brief pause as if her gut tells her something's up before she chooses to trust Jeremy's Digimon partner. The two head to the factory via the boiler room passage into the sewer, where Aelita receives a phone call from Jeremy just as they enter the elevator. Jeremy informs her of the Tower but sounds surprised when Aelita informs him she's already on her way after Shelley came to pick her up, even moreso after she remarks on him finally being able to reach her as this was the first time he's tried. The Shelley next to Aelita reveals himself to be one of XANA's polymorphic spectres when it electrocutes her, knocking her unconscious and ending the phone call. Jeremy panics, easily deducing what just happened, and calls the others to race to the factory pronto.

The Shelley clone sends Aelita to the Desert Sector to an awaiting William, and the other Lyoko Warriors arrive not long after. The clone is waiting for them when they enter the lab, and Gumbo and Leon offer to stay with Jeremy to fight the clone while he sends the rest off to Lyoko. While Odd and Ulrich head off towards the activated Tower to take care of it, Yumi and Florence square off with William, who is using a smoke-based telekinesis on Aelita when they find him to carry her off towards the edge of the sector. In a brief exchange between Yumi and Jeremy, it's revealed that William's smoke powers on Aelita's Avatar interferes with his attempts to manually devirtualize her. Meanwhile, Shelley's clone is displaying all of his Kamemon abilities in battle with the other two Digimon, which Jeremy speculates is because XANA got a good look at his code back when he came in contact with the Jeremy clone. William continuously struggles to keep a hold on Aelita and fight the duo on his back, and Jeremy frustratingly keeps trying to manually devirtualize her the moment she's broken free only for his efforts to be undone every time William's smoke grabs her again.

We get a bit of Ulrich and Odd fighting with XANA's monsters on their way to the activated Tower. After that, we return to Yumi as she engages in battle with William. However, this proves to be a distraction so that Florence can sneak away with Aelita on the Overwing. They manage to put in some distance before William catches on and uses Super Smoke to catch up to them, charing and firing an energy slash from his blade to destroy the Overwing. Yumi rushes in to help both, but William uses the distraction to knock her down and take her war fans from her. Florence recovers, but she's prevented from joining in to help Yumi by the arrival of William's black Manta and needs to look after the still weakened Aelita. Jeremy informs Ulrich and Odd about the situation, both having just about cleaned up the site outside the Tower at this point, and Ulrich forfeits the race to Odd so he can drive back to help Yumi. As Ulrich races back and jumps off the Overbike before it rams into William (or tries to; he uses his blade as a ramp to veer the vehicle away from him), Odd enters the Tower and talks himself through the procedure as he enters the LYOKO code for the first time.

On Earth, the Shelley clone vanishes mid-attack. Around this time, Ulrich has just barely managed to fight William to a stand-still, but this has given Yumi, Florence, and Aelita a chance to recover and join Ulrich. Finding himself outnumbered and the attack on Earth foiled, William chooses to retreat. Later on, the team discuss the implications that XANA's spectres can scan and copy Digimon's abilities. After some talking, they agree that they should try communicating with other so-called "DigiDestined" who may be affected by XANA's spread through the rest of the Digital World. The Digimon recount a tale of the first team of DigiDestined in the modern era and how they defeated infamous threats such as the Dark Masters, Myotismon, Apocalymon, and Diaboromon. Jeremy recalls a point in time when he was younger and just starting to get into computers, when he witnessed a battle between two large beings on the Internet from the Belpois family computer. Part of the story includes little Jeremy having sent an e-mail to one of the two humans overseeing the hero of the battle, that human being identified in present day as Koushiro "Izzy" Izumi. The Lyoko Warriors agree to contact Izzy to help coordinate with other DigiDestined and work out how to fight XANA back together. Some friendly small talk wraps up the episode.

The episode opens on the roads of suburban Paris, with Michel Takaishi giving Izzy and Tentomon a ride in his motorcycle's side car, Izzy having a closed and unidentified bundle next to him. Izzy thanks Mr. Takaishi for giving them this ride, and some friendly chatter between the characters help to further establish for the readers who they are and that Izzy and Jeremy have sent each other a couple of e-mails by now before Jeremy agreed to let Izzy come and see this supercomputer of theirs for himself. By the end of their conversation, the Renault Factory is just ahead. Meanwhile, the Lyoko Warriors are admiring the new and improved Forest Sector, with Jeremy giving most of the credit to a modest and flustered Shelley, claiming that all he did with this particular sector's recreation was supervising and a bit of proofreading. After a bit more time is spent looking over the sector's new features, Jeremy gets an alert from the factory's security system and checks to see that their "guests of honor" have arrived; Shelley hops to Earth to join them. Mr. Takaishi waits in the factory cathedral, having brought a long book to pass the time, while Izzy and Tentomon take the elevator down to meet Jeremy and Shelley in person for the first time.

After a scene of pleasantries, there's a montage of Jeremy showing Izzy various supercomputer hardware and explaining it, including the supercomputer tower itself. At one point, he also shows Izzy entries from Franz Hopper's diary, which includes acknowledgments of the Digital World and Digital Monsters, as well as references to heated disagreements with a high-ranking member of Project Carthage named Mark Hollenback. As they discuss matters Jeremy has presented Izzy with and how other DigiDestined may be affected, Izzy provides Jeremy with the building blocks for a secure virtual Cyberspace Room which Lyoko Digimon would be able to freely enter and exit through Internet-enabled monitors as well as text their partners. Jeremy resolves to load and build it onto a special restricted-access portion of the supercomputer's hard drives that he has access to, as well as create secure gateways in the Cyberspace Room that allow their Digimon freely in and out of the sectors of Lyoko as well. About this time, the Superscan picks up an activated Tower in the recreated Forest Sector. They've only started to ponder what XANA could be planning when a spectre emerges from the wires within the lab and invades Izzy's body. Izzy struggles and fights off the spectre, and Jeremy recalls that XANA cannot possess those with experience being digitalized; Izzy has gone to and from the Digital World plenty of times by that point. However, the Tower that spawned that spectre does not deactivate.

Jeremy warns the others on Lyoko, pointing them off towards the other end of the Forest Sector. As the heroes on Lyoko are on their way to the activated Tower, someone leaps down from the rafters above the lab: Mr. Takaishi, possessed by XANA. Izzy and Tentomon are understandably reluctant to fight him, though Jeremy assures them that XANA provides his vessels with plenty of invulnerability for their battles with the heroes. Mr. Takaishi tries to attack the heroes on Earth to get to and sabotage the supercomputer, but the two Digimon present engage him. The heroes on Lyoko near the activated Tower to find William guarding it, flanked by two Krabs. The humans engage William, who clearly wants to try whittling them down until he can take one unopposed and toss them over the sector edge. The three Digimon accompanying them, meanwhile, engage with the Krabs. After a fair bit of battling in both worlds, and quips from different sources here and there, William has managed to devirtualize Yumi and Odd and is already making his move towards Aelita. With Krabs dealt with at this point, the Digimon tell Ulrich to go to the Tower while they keep William from running off with Aelita. Yumi and Odd have joined the battle against Mr. Takaishi without question as Ulrich reaches the Tower, and the man is freed from XANA's control shortly after, passing out but otherwise being okay. Jeremy is able to devirtualize Aelita while the Digimon have William distracted, and they make a tactical retreat to the now deactivated Tower now that there's no more reason to fight. When the humans and Digimon all meet in the lab, Leon takes one good look at both Izzy and Tentomon and says he knows them but doesn't remember how. Izzy suggests that if they have met before, it's possible that Leon's memories still haven't returned after the Digital World reboot.

Mr. Takaishi comes to on a cot in the factory cathedral, and the others proceed to give a fairly simplified explanation of what happened to him. Jeremy and Izzy both agree that XANA's ability to possess humans is something the other DigiDestined should be warned about, though the fact that the DigiDestined themselves are immune should be an advantage not to take for granted. Izzy goes to the bundle he left in the motorcycle's side car and opens it, retrieving an egg with a pink-grip Digivice attached from inside. He hands it to Aelita, explaining that it is her partner and a gift from "an old friend of ours" named Gennai. Gennai apparently hadn't known about Aelita until just about a year ago when he picked up on Jeremy falsifying her online records to enroll her at Kadic, and even then he was further delayed in securing her a partner due to the attack of an evil doppelganger (which is apparently a whole other story). He then pulls out a tablet device that he calls a Digi-Tablet, giving it to Jeremy with the explanation that he built it as a prototype for a series of Digivice-synchronizing communicators he intends to build for himself and his friends. Jeremy is free to program the tablet as he sees fit. All agree to keep in contact, with Izzy offering to help direct Team Lyoko to XANA's "Replikas", as they've been calling them, once they've built their digital submarine. After some parting words, we end with Aelita in her dorm at night as the egg hatches and she quietly and happily greets the fresh-form Digimon that emerges.

The next episode has the Mountain Sector recreated, finally completing Lyoko's full rebirth. On that same morning, Jeremy receives a package from Izzy at school containing installable drivers for a proper Digivice port and a pair of USB ports, as well as a 3D printed replacement case for the supercomputer keyboard with the proper holes to fit the additons. Jeremy and Aelita decide to switch off the lab interface to dismantle its keyboard to begin installations, and Jeremy reroutes some of the supercomputer's energy to engage a temporary "soft lock" on all the Neutral Towers on Lyoko that should last a good few hours so XANA cannot catch them unprepared. As the other Digimon enjoy their newly programmed Cyberspace Room on their down time, Shelley hops into the new Mountain Sector to quickly double check a few build codes on Jeremy's behalf. As he trots along, he quickly spies William flanked by a few monsters focusing on one of the Towers, which Shelley realizes is in attempt to channel XANA's energy into it to override the soft lock. He attempts to retreat unnoticed to warn the others, but William easily catches and ambushes him, forcing him to endure in battle against him and his monsters alone. This lasts a while until the other Digimon jump in to the rescue right as William has Shelley cornered, saying they came when they wondered what was taking him so long. With all fighting back against William together, they soon get the upper hand and ultimately drive XANA's general away. Once Jeremy and Aelita finish their installations and reactivate the interface to contact them, the Digimon inform the pair of what happened and are congratulated on their victory.

At the start of the next episode, Jeremy, Aelita, and Shelley have been working on some of the final steps for the creation of the team's new submarine. They are quite eager to unveil the end product when it's ready, and Aelita's Digimon, now a Tapirmon, watches in fascination. The Digimon has since been nicknamed Munin, which Aelita explains they picked from a book on Viking gods and legends that her father read to her as a little girl, which she had been reading to them in turn in their free time together. Since nobody seems to be willing to officially name the sub before it actually exists, Odd codenames it "Melanie" after a girl he likes; this gets a few laughs, but nobody disputes this. It's late at night, so the team set off to go to bed. Jeremy says he and Aelita still have some last minute touches they wanna get done before the sub's official christening tomorrow, but Shelley chimes in that he can do the last minute touches from his Tower interface, insisting that both get a good night's rest. He can nap in the morning while they have their classes.

Later on, Shelley is curled up in his shell and snoozing away in the Sector Five Tower, where he had set himself up on the still open interface. A beeping from the interface wakes him up, and he notices the display is showing a troubling number of XANA's monsters converging on the section of Sector Five that Aelita had designated their submarine's hangar. He sends a quick S.O.S. to Jeremy, who sends a text back saying that class will be over before too long and asking him and the other Digimon to be the incomplete sub's first line of defense until their human partners can get there. Shelley contacts the others in the cyberspace room, telling them about the situation. As Creepers converge on the sub's hangar, the other Digimon arrive at the edge of the sector, Shelley hurries to usher them towards the Core Zone elevator, where a squad of Creepers have already started firing upon "Melanie's" outer shielding. Battling is done, and the Lyoko Digimon manage to take out most of the Creepers. But then an animalistic shriek is heard from above, and William descends from above, his black Manta ride flanked by two regular navy Mantas.

The next bit of story is them struggling to both protect "Melanie" from as much onslaught as they can while simultaneously enduring William's assault. Then Jeremy checks in, reporting to their relief that the Lyoko Humans are already on their way to back them up. When they arrive in the hangar, they converge on William, freeing the Digimon to properly tackle and wipe out the Mantas, just moments before "Melanie's" shielding would've given way. Seeing the Mantas have fallen so close to victory, William blows everyone back and launches himself on top of "Melanie" to try to get a strike in himself, but Aelita manages to conjure one large Energy Field that wears her out but manages to devirtualize William just in time. With the site cleared of hostile forces, Jeremy is able to complete "Melanie's" programming, and a fully functional flying submarine with detachable pods now rests docked in the hangar.

The whole team meets in the lab to discuss the sub's future, including the name, given "Melanie" was a codename only. No one can seem to come up with something good, until Aelita brings up the Viking book she'd been reading to Munin, pulling it out of her bag. She flips to one page, pointing out a mythical tall ship called the Skidbladnir that could sail on land and always reached its destination no matter how the wind blowed. The team agrees to name their new ship the Skidbladnir after it, or the Skid for short. With the newly built and christened Skidbladnir, the Lyoko Warriors are ready to travel out into the rest of the Digital World. Jeremy says he will be informing Izzy about the submarine's competition and naming, as well as their plans to test the new vehicle soon.

The episode in which said test occurs has Jeremy initially try to limit it to a dry test out of concern, but the others (including Shelley) manage to talk him into permitting a full dive with the Skid to really test what it can do. Unfortunately, a bug in the sub's navigational system leaves it unable to find its way back to Lyoko's Virtual Shell until Jeremy can go grab the subprograms to debug it from the school, so he leaves Shelley to monitor the situation while he leaves. Meanwhile, the Skid is targeted by a group of viral Deep Savers responding to a bounty on the ship placed by an "unknown client" (obviously XANA), but the Lyoko Warriors are able to evade and eventually chase off the bounty hunters by the time Jeremy returns. Upon debugging the navigational system, Jeremy is able to direct the Skidbladnir back to Lyoko before its engines run out of power. Despite the complications, the team ultimately declare their test an overall success. The next couple of episodes include ones of the Lyoko Warriors exploring past the Digital Sea, fighting XANA's monsters abroad, and getting pulled into other Digital World shenanigans. One possible subplot for now or later could have Ulrich encountering a criminal Digimon harassing a village for "protection money" and challenging them to a fight to get them to leave the villagers alone.

The first Replika the team explores in-depth is located in the jungles of the Folder Continent, and they discover a near faithful recreation of the old Forest Sector inside its Virtual Shell. However, they cannot exit the Digital World through use of their D-3s when initially entering through the scanners, and entering it with their D-3s leaves them without the guidance of Jeremy and the supercomputer's resources. To that end, Jeremy studies how the Digimon freely jump into the material world while retaining their digital nature, leading to the creation of the "Translation" program, allowing the Lyoko Warriors to appear for a limited time in the real world as their Digital Avatars, powers and everything, by docking the Skid to a Tower. The team returns to the Forest Replika and sends Odd, Aelita, Gumbo, and Munin on a mission to find the supercomputer XANA used to create it, which they discover in an old Amazon rainforest research facility. They discover cybernetic spiders being created in the facility and attempt to shut it down, but William in the Digital World foils their attempt by using the Annex Program XANA gave him to put the Skid-docked Tower in XANA's control. XANA "de-translates" the heroes moments before they can damage the computer hard drive.

The Lyoko Warriors later return to the Forest Replika again for round two, this time successfully destroying the supercomputer as they now know to keep William away from the docked Tower. Around this time, there is also a subplot for one episode of a bug in the supercomputer that somehow causes Gumbo to go through the scanners, being converted to matter and coming out in the real world in an organic version of his normally digital body. This development becomes a race against the clock to re-digitize him, as being a Digimon in material form makes him unstable and threatens to completely disintegrate him if the effects of the bug aren't reversed in time. Some time after the destruction of the Forest Replika, Izzy forwards an e-mail to Jeremy from an American DigiDestined named Willis, reporting that Willis and his Digimon investigated an abandoned research facility in New Mexico and were able to destroy a Replika-generating supercomputer within. However, they had a brush with a small army of Kankrelats on facility grounds along the way. Jeremy speculates that XANA must've copied the translation program when he took over the Tower using it so that he can use it on his monsters. Willis also reports finding a mass production of computer chips when he infiltrated the facility, claiming he intends on studying one and forwarding anything he figures out from it.

From here, there's more episodes focused primarily on either taking down XANA's Replika supercomputers or the Lyoko Warriors getting swept up in other Digital World matters between those missions. With each Replika they discover, and ultimately destroy, Jeremy scans them for the hypothetical Tower he believes XANA must be using to sustain his long-term possession of William, but no such search so far proves fruitful. One subplot would have Aelita away from Kadic to take part in the final round of the DJ contest she entered early on in the series, and the Lyoko Warriors back on the home front would have to manage without her. Spoiler alert: she wins.

At some point, Willis would contact Jeremy to tell him he uncovered a masked shipment of those computer chips and managed to trace it to a decommissioned facility in Siberia simply known as "Union Base". When Jeremy detects a Replika in the Union Base hard drives and pinpoints its location in the Digital World, the Lyoko Warriors set off to deal with it. They discover that the chips from New Mexico are being used, among other components produced in other Replika supercomputer sites, to build bulky combat-ready robots. They're stopped from doing much when William is translated on site to intervene, but Aelita takes advantage to copy data from the activated Tower to be traced back to the elusive Tower controlling William. After some fiddling around with the code Aelita acquired after the mission is over, Jeremy pulls out a finger-sized computer chip and explains to Shelley how XANA once used it in conjunction with an activated Tower to control Aelita. Cross-referencing the leftover data on the chip with the data from William's translation Tower, he's finally able to follow the trail to a Replika generated somewhere in Switzerland, which somehow seemed to elude his scans for Replikas prior.

The Replika itself is deep in the far end of the Digital Sea, but the Virtual Shell is significantly different than any of the others they had seen so far. Aelita calls it "less pretty" than Lyoko's and "more like a cortex". What's more, inside is a virtual environment unlike Lyoko or any other the other Replikas, looking more like a constantly shifting industrial site than anything else. Unfortunately, the unstable nature of the landscape makes it easy to be crushed by the environment, and the fundamentally different code of what they call the Cortex means that they do not automatically rematerialize when devirtualized. Aelita locates the core interface of the Cortex and just manages to send data Jeremy's way from it before she's devirtualized as well, though not before discovering a mysterious photo of her father in the adjacent supercomputer's files. Jeremy is able to work the data he gets into a Cortex-based rematerialization program and bring his friends back.

In preparation of round two, Jeremy and Aelita manage to program a new vehicle called the Cortexian Rolling Articulating Spheroid Techto-compatible Mega-Multipod Vehicle. Or for short, MegaPod. The MegaPod allows the Lyoko Warriors to navigate the constantly shifting landscape of the Cortex with greater ease, and they are able to locate the Tower that Jeremy traced William's data to. With all four going in after the Tower, the Digimon partners stick around the Skidbladnir at the more stable edge of the Cortex to protect it. Naturally, William is sent to stop the Lyoko Warriors and fights as hard as he ever has against them. Then things get weird when Jeremy picks up on massive amounts processing power being drawn from all other remaining Replikas all over the Digital World. Odd is the one to make it into the Tower and deactivate it. But just as he's starting to come back, a colossal volcanic beast emerges from the Digital Sea and advances on the Skid. The Digimon mount the sub's defenses, but they barely scratch the behemoth. William, still under XANA's control as long as he remains in the Digital World, takes advantage of the distraction to devirtualize the remaining warriors on the battlefield. But he himself is distracted in doing this, and Odd returns to get the jump on him and devirtualize him with a Laser Arrow to the back. Odd scrambles to get back to the Skid before the giant monster can attack it, but he forgets in his panic about the Cortex's shifting landscape and is quickly taken out. The monster smashes at the sub with its sword arm, knocking it into the Digital Sea in a heavily damaged state and leaving the fate of the Digimon uncertain.

On Earth, the Lyoko Warriors having filled William, now free, in on what had happened since the Scythozoa captured him. Renamon has also been called back to fill William in on everything he'll need to know for a smooth transition between the "acting William" and the real William at school. The others thank Renamon for the cover before Jeremy opens a port back to the Digital World on the Digi-Tablet. Before leaving Renamon reassures them of Digimon being tougher than they look and advises them not to count their partners out just yet. As they return to school, sans Jeremy who stays behind to keep scanning the ocean for signs of the sub, the group discuss matters going forward such as William's integration back into school life and the whereabouts of their Digimon partners.

The next episode opens with the battered and barely functioning Skidbladnir floating aimlessly in the deep blue of the Net Ocean. Shelley has been keeping comms open with the NavSkids so that he and Munin can keep chatting idly with the other Digimon as they're all feeling really weary by this point and want to remain as alert as they can. As they discuss their predicament, it's revealed that it's been several hours since the volcanic giant damaged the Skid and sent them into the ocean. They wonder how their human partners are doing and whether or not they were successful in freeing William, as Shelley notes that the comm channel with the supercomputer has been down for some time. Gumbo has been mumbling delirious ramblings throughout, and one of them ends up being a wearily cheerful greeting towards a Whamon. Moments later, that last one is proven not to just be delirium on Gumbo's part when something big comes in contact with the under side of the sub and starts pushing it upwards.

On the shore of File Island not far from Factorial Town, Izzy and Joe watch the sea. Izzy thanks Joe for taking the time to help, as Gomamon spreading word around the sea should help find the missing Skidbladnir much faster; Joe reassures him he's got a good few hours before his Saturday classes. Gomamon pops out of the water to report that Whamon was seen bringing in something really big, figuring it's probably the sub they're searching for. In short time, the damaged sub is shoved out of the ocean and onto shore, and Gomamon digivolves to Ikkakumon to start prying open the already pretty busted NavSkids, starting with the one containing Leon. Leon's already pretty out of it, but he's just alert enough to see Izzy's Digivice light up as Tentomon becomes Kabuterimon to help out; he mumbles vaguely in recollection of that light before he passes out from lightheadedness and possibly (Joe's speculation) decompression sickness. As the rest of the Lyoko Digimon are recovered from the Skid, Joe offers to provide medical attention while Izzy sends an e-mail to bring Jeremy up to speed.

Morning arrives at Kadic, and Aelita checks in on Jeremy, who has been up all night working on the search for the Skid and its passengers. Aelita expresses her concerns for Jeremy, as the prolonged absence of Shelley seems to have caused him to slip back into his old unhealthy sleeping and eating habits. Jeremy passes on Izzy's report, which also claimed that they were close enough to the appropriate industrial resources that they could repair the Skid on site. This is regarded as good news, but Jeremy insists on staying on the job to help supervise repairs remotely and coordinate their return to Lyoko. Aelita goes for breakfast and informs the others of the news. When William shows up to an unintentionally cold greeting, he takes a hint and goes sit by himself, which prompts Aelita to scold the others for still treating him like an enemy. Ulrich judges him for having been caught by the Scyphozoa in the first place, but Aelita refutes this point by reminding everyone of the multiple times it had captured her. The others finally agree to be more civil with William but decide he should never be allowed into the factory anymore.

Shelley comes to and finds that he and the other Lyoko Digimon are on makeshift beds in Factorial Town, and Gomamon is looking after them in wake of Joe having left for his Saturday classes. According to Gomamon, Shelley was in comparatively better condition than the others, attributing it to Shelley being a fellow Deep Saver. Andromon steps in to reveal that he has been lending full use of his factory towards repairing the Skidbladnir per the e-mailed specifications of Jeremy, partially as an act of good will towards the DigiDestined but also to help out an old friend; Andromon and the Kamemon currently known as Shelley know each other. In the assembly area, Izzy is overseeing repairs to the cockpit control panel when Tai and Agumon arrive, accompanied by a Pagumon. Izzy questions the Pagumon's presence, to which Tai presents a silver-gripped D-3 Digivice as he and Agumon explains that Pagumon is allegedly "looking for someone" but "doesn't know exactly who yet." They assume this to mean he's some undiscovered new DigiDestined's partner. Pagumon acts strangely familiar towards the three (Agumon especially) but stays cryptic about how it is he already knows them.

Izzy finishes patching up a few connections in the control panel and then calls out Jeremy's name, saying he's just finished putting the transmitter back together. Jeremy confirms they have connection, as Tai remarks in confusion that he's hearing him in Japanese. According to Izzy, the Digital World is translating for them in real time. Jeremy says that repairing the Skid transmitter to allow for direct communication should allow for the repair process for the rest of the sub to go a lot smoother, also thanking Izzy for e-mailing him the map of File Island. When Izzy says that he and Jeremy had been corresponding on sub repair procedures for the past few hours or so, Tai questions the time in France and when Jeremy has last slept; Jeremy stays silent. Izzy takes the hint, warning Jeremy from personal experience that pushing himself so hard as to deny himself sleep can do more harm overall than good. Jeremy admits he's just really worried, to which Izzy sympathizes but counters that working himself to exhaustion won't do their partners any good.

About this point, Jeremy warns them that XANA must've picked up on the Skid's transmission frequency as well, as his monsters are beginning to show up on File Island. He asks how the other Digimon are doing, and Shelley shows up at that moment to report that the others are conscious at this point but still pretty out of it. He'd just popped in to warn Izzy about the distant approach of XANA's monsters when he heard Jeremy, and both are quite happy to hear each other again. The main concern is that one ultimate-level Digimon, two rookie-level Digimon that can digivolve, and two that can't, they may not have quite enough muscle power to fight back the whole army's worth of enemies approaching. Shelley's the one to point out that since the Skid's transmitter is working again, Jeremy should be able to virtualize the Lyoko Warriors directly to Factorial Town. Jeremy assures them the others will be on their way and encourages them to stand their ground until then before quickly hanging up. Izzy, Tai, and Agumon go to fetch Tentomon before both DigiDestined give their partners the energy boost to digivolve into champion. Leon is sort of awake and sees this; with greater certainty this time, he again recognizes the light from the Digivices.

Back in France, the Lyoko Warriors meet in the factory lab, where Jeremy fills them in the Cliff notes version of the situation on File Island and tells them that the four of them better get going. "You mean, the five of us?" It turns out that William picked up on the team's hasty retreat to the factory and followed, wanting to help them save their friends as well as get some payback on his former possessor in the process. But Yumi refuses, claiming William would just be a liability, but Jeremy proposes William stay on standby in case backup is needed, since they don't have time for any arguments now. On File Island, Greymon and Kabuterimon are holding their own fairly well, given the situation. However, a MegaTank arrives and quickly knocks Kabuterimon out of the battle, and Greymon follows suit shortly after. As XANA's monsters advance some more, Yumi and Aelita appear in the sky and drop down to quickly join in the fight with Ulrich and Odd arriving moments later.

After all the active Lyoko Warriors have entered the battle, Leon confidently marches right onto the scene looking much better now. He tells the 1999 DigiDestined that he managed to draw strength from their Digivices, just as he has before. Their light has again reminded him of who he truly is: a champion of justice who is always honored to fight by their side. Drawing energy from his own partner's Digivice, Leon digivolves from Elecmon to Leomon, though Tai and Izzy have already figured out from his pre-digivolution words alone that he is the same Leomon that they know, and he quickly joins the fight alongside a particularly surprised Ulrich. The battle continues to its conclusion, and Aelita steps inside to further assist on-site with the Skid's ongoing repairs. Leon has since reverted back into an Elecmon, but it's already known to everyone (including himself) that he is the individual the 1999 DigiDestined knew as Leomon. During the downtime, Leomon's final moments before his real world death are vaguely discussed; it's speculated that Leon's data made it back into the Digital World through the still open distortion, as most other cases of Digimon dying in the real world did not have their memories backed up before the reboot (Wizardmon is cited as an exception, as his death and revival are described as a "particularly unusual case").

As current events are discussed, everyone's glad enough that the XANA attack on Factorial Town is done and over with, and Agumon casually comments on not knowing how that could've gotten worse. Cue the giant volcanic monster beginning to emerge from the sea surrounding File Island, the giant being dubbed the Kolossus by Odd. At the factory, William watches with Jeremy, asking for clarification on the team's Digimon friends and showing understanding when Jeremy explains how they were lost while helping with the mission to free William from XANA. William admits that he messed up, but he asks for a second chance to do better. Not just to get back at XANA but help pay back the digital companions who risked themselves to help save him. Knowing the Kolossus is something the team will need every bit of help they can get with, Jeremy decides on the spot that he's sending William in, granting him that desired chance. On File Island, the Lyoko Warriors are faring poorly in any attempts to slow the Kolossus on its slow advancement towards Factorial Town. Yumi and Odd are devirtualized, but not before Ulrich manages to deduce that the Kolossus has two weak points that need to be attacked, presumably simultaneously, for the giant to be stopped: a bigger one on its head and a relatively smaller one on its sword arm.

William arrives and, instinctively tapping into his XANA-given Super Smoke ability, swoops in to save Ulrich from the Kolossus's massive sword arm swing. The two end up working together to take down the beast, with William striking the head target at the same time Ulrich strikes the arm target. The Kolossus nearly falls on Ulrich as it goes down, but William is able to Super Smoke him out of the way in the nick of time. The giant's volcanic parts cool down as the Kolossus permanently stops moving. Once the dust clears, everyone still in the Digital World regroups at Factorial Town, where Pagumon is quick to jump forward to claim William as the one he's been looking forward. Tai takes the hint and hands William the new Digivice, at which the latter's Digital Avatar generates a belt loop for it like the ones the others' Avatars have gotten. After a bit of dialogue relevant to William and Pagumon's partnership, time skip to when repair work on the Skidbladnir is just completing. Parting words are exchanged, after which Jeremy Energizes all on-site Lyoko Warriors into the sub for its triumphant relaunching. Once the Skid has parted into the sea, the DigiDestined and partners still there are left wondering what they're supposed to do about the gigantic "corpse" on the beach.

With the whole Lyoko Warrior team regrouped at the factory, they lament how this may not be the last time they see a Kolossus, even if the fact that it requires processing power from every Replika to generate means it'll probably be a very rare sight. Adding onto that, the sheer number of Replikas that there are has the team concerned that a one-at-a-time method of dealing with them may take too long, even if other DigiDestined around the world are helping. What's more, both Jeremy and Aelita can't help but feel there's something off about that Cortex "Replika" they discovered William's control Tower in, leading them to speculate that it's not even a Replika to begin with. Furthermore, Aelita brings up the mysterious photo of her photo she found in the supercomputer of the Cortex and wonders what it could possibly have been doing there. They conclude that they need to explore the Cortex further to try and figure it out, but Shelley adamantly pushes for Jeremy to get some good sleep in first. William thanks the others for the second chance, and they finally agree to fully integrate him back onto the team. But they still want to keep a close eye on him going forward until he's worked enough to fully earn their trust back, which he accepts. He's got plenty of bonding to do with his new partner in that time.

William is back on the team, along with a new Digimon among their ranks, but XANA is still a long way from being defeated. And what mysteries does the Cortex have in store for the Lyoko Warriors? On top of that, they still don't know where the elusive Franz Hopper is hiding. Whatever the answers to their still lingering questions may be, they'll move onward and figure them out together.

End of Arc One.

As William tries to get back into the swing of school life while getting to know his new partner, Jeremy has been studying the data Aelita copied from the Cortex. What confuses him is how it seem's fundamentally similar to yet different from Lyoko's data, as if someone took the raw building blocks and tried putting them together themselves without the instructions. Meanwhile, the Subdigitals concert for which Aelita will be opening for is fast approaching and will be held on stage in Paris. Odd had solicited Jim's help in convincing Princiapl Delmas to let the students go watch their fellow classmate in her first big gig, eventually wearing him down. Jeremy's reluctant to leave the supercomputer for such a major downtown trip while there's still so much work to do, but then Shelley reminds him that this is for Aelita in addition to the fact that as Jeremy's Digimon partner, he can freely jump to and from Lyoko through the Digi-Tablet to handle any work or emergencies while they're away.

The arrival at the concert hall and opening act go well fairly well, with Aelita's friends in the front row cheering her on. But then backstage afterwads, the band's manager, Sophie, is possessed by XANA and incapcaitates Aelita to sneak off with her unnoticed by almost everyone. Jeremy manages to sneak off after her unnoticed, leaving the Digi-Tablet behind in the process, and he texts Yumi to inform her of the situation and have her forward it to the others. Due to time constraints and the less likelihood of all of them sneaking out of the concert hall together unnoticed, they agree that they're going to have to take the risk and jump into Lyoko with their D-3s. Someone is needed to stay behind to watch the tablet as well as cover for the others, and William surprisingly agrees to stay behind to do it as he genuinely wants to work to earn their trust back. However, at the same time, they end up meeting someone from William's past. Namely, Catherine Deneuve, the very girl William got expelled from his previous school for posting love letters to all over the campus (including, apparently, the principal's windshield). Catherine is not happy one bit to see William again after that past embarrassment, but she's willing to cooperate once she figures out he's performing important DigiDestined duties, having a Digimon partner of her own. And then Milly and Tamiya spring up, also possessed and trying to get the Digi-Tablet to strand the Lyoko Warriors, leading William, Catherine, and their respective Digimon partners to fend them off. In the midst of battle (set to the tune of the Subdigitals' song "Break Away" {Note to self: AO3 terms don't allow full song lyrics; only allude to what song is playing}), William's partner digivolves from a Pagumon to a BlackAgumon.

While Jeremy evades the possessed Sophie in the factory and the others fight the news kids at the concert hall, the gang on Lyoko run into the Scyphozoa while finding Aelita and tracking down the activated Tower. Aelita assures the others that the new Way Towers are unresponsive to the XANA Code that she previously deleted the sectors with while possessed, but that just means the Scyphozoa has other intentions. As the encounter continues, they conclude that it wants to get Aelita thrown in the Digital Sea, whether by possessing her to throw herself in or by chucking her down itself. Lyoko Warriors need to fight the Scyphozoa off of Aelita while simultaneiously avoid laser fire from XANA's other monsters, given devirtualization in their current digital states would be permanent. By the climax, the Scyphozoa eventually does succeed in its mission and flies away. But to the others' surprise (after the initial horror of seeing Aelita take the dive), the monsters neither leave nor continue fighting, rather they go to the edge of the sector as if waiting. Just as they're wondering what happens from there, a bright purple and blue orb rises up out of the Digital Sea and begins dodging the sudden rain of laser fire to the best of its abilities as the monsters still present begin shooting at it.

The team unanimously agrees that if XANA wants it destroyed, it must be important and start picking off the monsters to give the orb some leeway. It arrives at the surface of the sector and deposits Aelita, pulls herself up while identifying the orb as none other than her father, Franz Hopper himself. Hearing this, the other Lyoko Warriors double down on taking out the rest of the monsters as Hopper makes his retreat into the Digital Sea as of completing his mission. The moment everything has quieted down, the group head to the Tower to deactivate it, saving Jeremy on Earth in the nick of time. As Jeremy and Aelita carry the unconcious Sophie away from the factory and back towards the concert hall, they talk about how Franz Hopper is still out there watching after his daughter. As soon as Sophie starts coming to near the hall, they gently put her down on the nearest public bench and put together a story of how Sophie apparently needed some air and the two had offered to walk with her before she blacked out; the disoriented Sophie accepts their claims. Back at the concert hall, Catherine admits that William has changed for the better far more than she'd have expected from him and that she's willing to move on now. Of course, she still returns no feelings for him, but she's willing to stay on civil grounds with him, which William graciously accepts. BlackAgumon declares he's already thought of a nickname for himself: Obsidian; Gumbo starts calling him Sid or Siddy for short, which Obsidan more or less doesn't disagree to.

The next episode to feature the Cortex has Aelita eager to start looking into the mysterious virtual landscape again, because she wants to get to the bottom of the photo she found of her father. Since the MegaPod only has four seats, Yumi elects to stay behind to continue working on a fundraising campaign she started to help a school in Kyoto that was recently damaged by an earthquake. Kiwi, meanwhile, also goes to the lab as a kind of time out in response to recent troubling behavior back in the dorms. Jeremy had since refined the MegaPod's code to imrove naviagtion and handling systems, as well as add engine power for potential turbo boosts and add a firing sequence. Odd takes the wheel of the vehicle, since the controls are similar to those of Galactic Invaders, a video game he's racked a high score on. Much to everyone's chagrin, he drives like crazy but still gets everyone to the center of the Cortex in one piece. However, in the core of the Cortex, the group falls into a trap that ends up devirutalizing all but Aelita.

Meanwhile, XANA possesses a robotic double Jeremy had created of Kiwi, Kiwi 2, and begins multiplying it in an attack on Kadic, derailing the fundraiser event in the gym and putting the student body in danger. The three that got thrown out of the Cortex mission decide they'd be more useful at the school and go to help fight the Kiwi 2 army. Surpisingly, Sissi of all people ends up being an incredibly helpful assist in the fight as well. Back at the Cortex, Aelita manages to establish a connection with the core interface and begins routing information back to Jeremy. As Jeremy looks over the coding for the Cortex, he notes it far more resembles the original data that Hopper had conceived when originally creating Lyoko from scratch than the copied data XANA used to create the Replikas, an observation that further confuses Aelita as she can't understand how her father could be connected to this place. Jeremy apologizes when noticing this seems to have upset her, assuring her that they will get to the bottom of this.

Before Jeremy can send Aelita back to the Skid to return to Lyoko and deal with the Tower there, a squadron of Kiwi 2 clones starts piling into the lab and going after him. Aelita returns to the waiting sub by MegaPod alone, but she cannot enter it without Jeremy energizing her. At that moment, the real Kiwi in the lab jumps up on the keyboard to escape his evil robot clones and just happens to press the right sequence of keys with his paws to complete Aelita's energization back aboard the Skid. Aelita doesn't know what's happening on Earth and decides she probably doesn't have the time to question it, so she quickly pilots back to Lyoko and finds the activated Tower, where the Lyoko Digimon have already fought off the monsters that were guarding it. She deactivates it, saving everyone under attack from the Kiwi 2 army. Jeremy saves all the data they copied from the Cortex to somewhere that won't get wiped by a time jump and launches a Return to the Past. Odd takes Kiwi's role in saving the day, no matter how accidental, as a sign that the dog should be given another chance. Later on, Aelita spends some time going through and feeling Lyoko, commenting how it feels more peaceful and serene than the chaotic and unstable Cortex.

The next episode has Jeremy and Aelita trying to decode a scrambled video file they recovered from the Cortex but overlooked in the chaos of the Kiwi 2 army invasion. They can make out that one of the two voices is that of Franz Hopper, and he sounds really mad at the owner of the other voice. By the end of the episode, they manage to decode the video and find Hopper, being addressed by his original name of Schaeffer, arguing with a man identified as Tyron about their work together post-Carthage. Schaeffer believes Tryon is acting selfish and that his actions could "finish Hollenback's work for him," while Tryon accuses him of being too small-minded to see the greater potential of their work. Schaeffer ends their partnership and walks off in a huff, and Tyron privately calls him naive before the video ends.

Tyron figure and his Cortex are regrded as a significant threat due to his actions and motivations counter to Hopper's and the Cortex providing XANA with additional resources. But due to the unstable shifting nature of the Cortex's landscape, it's deemed too dangerous to try to dock the Skid to the one known Tower and try infiltrating the real-world location of the supercomputer like with the Replikas. To that end, Jeremy and Aelita try to develop a virus that can penetrate the core of the Cortex and shut it down. They test a blank copy on the core of Lyoko, but it fails to beach the core's safeguards. Hitting a block, Jeremy reaches out to Izzy for help to see if his fresh perspective can figure out a workaround. Willis over in America is also consulted at points, given he did develop the virus that killed the New Mexico Replika, though he admits that his virus primarily succeeded because the supercomputer was already riddled with bugs that weakened its defense.

However, as the DigiDestined programmers make progress with the virus, various points of File Island start getting swarmed with what appears to be XANA's monsters at first, except they are darker colored. The Lyoko Warriors and the joint 1999-2002 DigiDestined teams investigate to do a little pest control and figure out what these "Dark Monsters" are trying to accomplish, but something doesn't seem right. When all Dark Monsters are defeated, a figure watching from up high begins appluading them in amusement, looking exactly like Gennai in black robes. Tai furiously explains that it's not Gennai but rather a rotton creep who played a part in the infection disaster from last year. Leon recognizes him when he shifts to "Digimon Emperor" form and is just as livid to see him back as the 1999 team. The "Dark Gennai" just laughs at their attempts at interrogating him for why he's there, claiming that despite his king's demise, he still has his own agenda but refuses to elaborate. He manages to escape through a portal, leaving a cryptic warning that they will meet again.

The virus is completed and ready for testing, Jeremy storing the data pretaining to it somewhere securely out of potentially wrong hands. The test on the core of Lyoko is a success, so a small team take off towards the Cortex with a loaded version. Back on the home front, the two Agumon take some time to chat together, in which Obsidian muses on how he didn't have anything to truly live and fight for until he became a Lyoko Warrior. He recalls a bit of life advice "a wise Digimon" once gave him, which Agumon almost instantly recognizes as words of advice he'd given to BlackWarGreymon. At Obsidian's knowing smile, he puts two and two together and expresses happiness at seeing the once lost (and once artificial) Digimon alive and well, but he also asks how he's back in the first place. Obsidian deduces that a small piece of his programming must have broken off his artificial body on the Digital side of the barrier it sealed and reconfigured into a natural Digi-egg, reflecting on the nature of his creation and speculating that his creator used so many Control Spires mixed together that it created a complex string of code that perfectly resembled that of a natural Digimon in mind as well as body. One that could reconfigure like a natural Digimon upon death.

Unfortunately on the Cortex side of things, the virus fails entirely and sets off an alarm that draws in the appearance of ninja-like beings that quickly take out the heroes. The team can only assume that both the failure and the virus and the appearance of the Ninjas suggest that the supercomputer generating the Cortex has undergone alterations, meaning that Tyron is still active and working on it. And the fact that he's well aware now that someone is trying to destroy it garuntees he'll be a major issue moving forward. Between that, XANA's continued operations, and Dark Gennai's mysterious activities, the Lyoko Warriors are going to have to stay on their toes at all times from then on. The good news is that the virus should work on XANA's regular Replikas, but it can only take them out one at a time. And there are still tons of them.

With Jeremy at his wit's end trying to figure out how to tackle the multiple dilemnas of Tyron's active work, XANA's goals for a robot army, and now Dark Gennai's mysterious intentions, Shelley is left wondering if there's some way he can find out more about Franz Hopper's past to better help his partner. To that end, Munin takes the Lyoko Digimon to an abandoned cottage in the northeast corner of the woods called the Hermitage, the home Aelita and her father had lived in before they fled to Lyoko. Munin explains that Aelita had taken them to see her old home a few times already, and the human Lyoko Warriors had combed through the old house multiple times for glimpses into Hopper's past. They propose they do their own digging around the place to try to learn a little more themselves, and Shelley is fully on board with the idea on the belief that a few fresh sets of eyes might even uncover a thing or two that the humans had overlooked.

Much of the episode would focus on exploring the Hermitage as both Munin and Shelley recall stories their respective DigiDestined partners told them about the place as well as Munin's own visits with Aelita. Someone eventually finds a strange lockbox with no obvious opening mechanism, which they quickly realize responds to piano music. When the Lyoko Humans are called in, Aelita is presented with the box and then proceeds to play the first two lines of Twinkle, Twinkle Little Star, and the box opens. Inside, Aelita finds a gold pendant in the form of a sailor's knot encirlcing the letters W and A, underneath which lies a folded note written by Franz Hopper under the impression that Aelita reading it means "something happened to [him]" (which technically isn't wrong). Franz gives a brief explanation of how he and Aelita's mother, Anthea, had previously worked on a project called "Carthage" but realized late into the project that their work would be used for sinister purposes. When they tried to escape, her mother was kidnapped and taken away from them, an event Aelita remembers occuring on a cold winter day in the mountains. Franz believes (as of writing the note) that Anthea is still alive somewhere but was never able to locate her. Franz hid in Boulogne-Billancourt and began teaching at Kadic Academy under the alias of Franz Hopper, secretly creating Lyoko using the same programs that he and Anthea developed together under Project Carthage in that time. But "they" managed to track him down there in time, and it was only thanks to the emergent program called Return to the Past that he could complete Lyoko in time. The note goes on to explain the pendant, saying that he and Anthea made each other identical ones and asking her to safeguard this one while tasking her with continuing his search for Anthea. The episode ends with the setup of this new mystery: the whereabouts of Aelita's mother, Anthea Hopper-Schaeffer.

At the start of another episode, Jeremy wants to go back to the Cortex to gather further data on Tyron's supercomputer to create a proper virus for it, as well as try to find more intel on Tyron himself in regards to his relation to Hopper and the alleged Project Carthage they both presumably left. Ulrich, however, bows out of the mission to participate in an interschool Pencak Silat competition that day. Jeremy is unhappy with him bailing but then takes a more understanding tone the moment he hears that Walter Stern, Ulrich's father, will be watching. Vague hints at how overly demanding Ulrich's father can be should've been sprinkled throughout the series by now, but here it's made made out perfectly clear for the readers. While Ulrich attends his competition, where he has to remember to try to be unpredictable while facing other humans in combat, the Lyoko Warriors infiltrating the Cortex again have been having an increasingly difficult time getting past Tyron's Ninjas and regroup to try to figure out how to proceed.

Back at Kadic, Ulrich has been advancing up the ranks, albeit barely as the guilt of having to bail on his friends and the pressure of his father watching is messing with him. Leon has been watching in secret to provide moral support, and he silently witnesses as Ulrich steps aside only to be confronted by Walter in private. Walter chastises his son on various things like his struggling grades, continued affiliation with presumed bad influences, and other things like Ulrich quitting the school soccer team (on that one, Ulrich reminds him that it was actually the team being disassembled due to budget cuts). Ulrich's wavering performance today is seen as further "proof" that he's just not putting in his all and needs reminded to do better, and the ensuing heated argument that hits its peak with Walter angrily lamenting having a failure of a son. Pushed to his absolute limit, Ulrich flees, losing his father so he can run off to the factory. Leon quickly follows, unaware in his haste to look after his partner that he is leaving a trail...

After an hour has passed since the last Lyoko Warrior's devirtualization in the Cortex, the team prepares to regroup and try again when Ulrich suddenly shows up, despite his surprised teammates' assumption he would still be at his competition. Ulrich only says he had to leave early and refuses to go into detail, insisting on going on the next mission in spite of concerns that his recent martial arts matches may have taken up much of his fighting energy already. The mission hits a snag early on into the Digital Sea, as Jeremy picks up a bug on the Skid's systems that it seemed to pick up in the Cortex, resulting in a faulty sonar. The situation only gets worse when a small squadron of XANA's aquatic monsters ambush the sub. And though the situation gets hairy, Ulrich refuses to bow out of the fight and "be a failure". In his reckless desparation to prove himself, Ulrich is lost at sea in the chaos of the ensuing battle and subsequent hasty retreat. The group frantically tries to track him down in the aftermath, but there's little they can do until the Skid's faulty sonar can be repaired.

One bewildered Walter Stern then shows up in the lab, having followed Leon's inadvertant trail to everyone's shock. He quickly starts demanding answers from the others while Jeremy scrambles to try repairing the sub's sonar, and Walter gets informed of the fight against XANA and Ulrich's involvement, as well as Ulrich's current predicament in the Digital Sea. Walter gears up to scold the Lyoko Warriors, but Leon quickly shuts him down and proceeds to hammer him with a long and detailed calling out over the negative effects all of his pressure has had on his son, whose last memory of his father could very well be hearing him call him a failure. Walter is stunned into silence before it sinks in that he might actually lose his son as a consequence of his actions pushing him away. As Walter stews on this while dialogue is exchanged, Jeremy detects a torpedo explosion somewhere in the Digital Sea and is able to triangulate Ulrich's location using that signal. The rest of the team, as it has been long enough that they can revirtualize, rushes to mount a rescue mission. Walter quickly follows them into the Scanner Room before anyone can say otherwise and waits there. Team Lyoko finds Ulrich on the last legs of his life support and surrounded by XANA's sea monsters, and they switftly take them out to allow Ulrich to safely dock his NavSkid to the main submarine. Ulrich is sorry for the trouble his recklessness has caused, but everyone is glad to have him back as they return to Lyoko to park the Skid in its garage.

A tired Ulrich rematerializes in the factory and is bewildered to find his father suddenly wrapping his arms around him and, even more shockingly, crying and apologizing. After everyone is back on Earth and some more talking is done, including Ulrich better explaining how the fight againt XANA has affected his life combined with the specific struggles with his academic curriculum that he'd never quite been able to ask for help in out of fear of being seen as weak, the Sterns reach a certain level of understanding and begin the long road to reconciliation. As much as Walter dislikes seeing children forced into this strange digital war, he recognizes that they're already in too deep now for him to try pulling any of them out of it. But out of a desire to make up for his past failings as a father, he promises to not only keep their secret but also provide any resources the Lyoko Warriors may need in the future. Jeremy weighs the risks to benefits and ultimately chooses to take Ulrich's father up on that, quietly cancelling the programmed Return Trip so that Walter can retain his memories and improving relationship with his son. After Walter has left, the team with Ulrich again go over the details on the past failed attempts to fight the Ninjas, who seem unusually adaptive compared to XANA's monsters. Ulrich seems to have an epiphany based on the lessons he's taken from his martial arts training, telling the rest of the team he has an idea for a future rematch at the Cortex, setting up for the next episode.

That night, Aelita has a nightmare about the day her mother was kidnapped and catapults out of bed in fright. Munin, who had been taking the effort each night to absorb Aelita's nightmares, watches apologetically from her computer. This particular dream was strong enough to resist their abilities and play in her subconcious uninhibited. The next morning, the Lyoko Warriors eagerly discuss in private their upcoming rematch with Tyron's Ninjas later that day, with Ulrich confident that he's figured out what they've been doing wrong. In class, however, they are caught off guard by the surprise new student, Laura Gauthier, who proceeds to smugly upstage Jeremy as top student right off the bat. But they put off focus on her in favor of setting off to Lyoko to handle matters in the Digital World. Out of nowhere, Laura herself shows up and innocently asks what they're all talking about, and they quickly improvise a story about helping beta test a new VR game called "Code Lyoko", which they're trying to keep under wraps while it's still in the beta stage. Laura seemingly buys their cover story and moves on.

At the factory as the gang prepares to set sail, Ulrich explains his theory on why the team can't formulate a concrete strategy when combating the Ninjas: unlike XANA's monsters, which are robots that operate on predictible algorithms, Tyron's Ninjas are actual people operating from the real world. He adds that he asked his father the previous night to look into Deckard Inc, Tyron's company, and subsequently learned that the company has investments in VR equipment. This all but confirms his theory as far as Ulrich is concerned. As such, like Ulrich does against martial arts competition, the Lyoko Warriors will need to "be unpredictible" when fighting the Ninjas. From Sector 5 to the Digital Sea to the Cortex we go. And one MegaPod ride to the core (with William tagging along as Super Smoke) later, they approach the interface in anticipation of the inevitable Ninja intervention. The fight isn't much less difficult, but the Lyoko Warriors manage far better this time when they start mixing things up and getting more creative with their combo attacks, which visibly catches the Ninjas off guard.

With a wide opening made, Aelita hops straight to the interface to log in. In the process of combing through the Cortex data for useful information, the stumbles upon a live camera feed straight into Tyron's lab. There is no sound on, but Aelita can see Tyron conversing with someone sitting at a side desk just off-screen. He hands the other a jump drive, and they lean back into view of the camera to grab it, revealing themself to be none other than Anthea to her dumbstruck daughter watching. She is wearing a pendant identical to the one Aelita found, futher proving her identity. The Lyoko Warriors are forced to retreat with the intel they now have when Tyron notices a webcam activated from within the Cortex and locks them out of the system. As the group back home discuss the things they learn, they decide to hold off on trying to take down the Cortex until they can figure out how Anthea fits into all of this. In the meantime, they can work on handling XANA's other Replikas throughout the rest of the Digital World. Back at Deckard Inc, Tyron speaks over the phone with a junior agent of his, Laura, who has suspicions of a small group of her Kadic classmates. As soon as he hangs up, Anthea remarks in confusion that she thought she felt her pendant vibrate. Perplexed and mildly disturbed, Tyron considers this impossible, as the one with the other pendant is supposedly dead, and Anthea reluctantly agrees that she may have imagined it. In her school dorm, Aelita sits in bed, squeezing her pendant with a lost expression on her face.

The next episode follows not the Lyoko Warriors but Willis and his Digimon in America. Willis managed to follow a faint trail of XANA's code to a decommissioned dam in the northern Rockies. He figures XANA has a Replika in the computer that operated the dam during its active days. Oddly enough, he and his partners approach the site with no apparent resistence to greet them. They do, however, find a lost girl the same age as Willis with blonde hair and a red jacket. Willis offers to help the girl out and guide her away, but then a Pulsemon shows up to frantically warn the group that the girl is not in control of herself. XANA attacks with the possessed girl when the ruse is exposed, and his Digimon are quick to defend him. The girl's name is Eva, according to the Pulsemon who identifies herself as her partner. Willis rushes into the dam's operations building to try to hunt down the supercomputer, all while the Digimon fend off the possessed Eva's attacks. Pulsemon talks about her history with Eva and how she started acting strange after a black puff of smoke from her PC overcame her. Willis has a copy of the virus he helped Jeremy and Izzy create, but he needs time to be able to run it on the dam's computer from the real world, and XANA-Eva is not giving him that courtesy, even with the Digimon working to protect him.

Some suspensful action later, Willis has managed to locate the computer terminal as XANA-Eva fights the Digimon (including a reluctant Pulsemon) trying to get to him. By the time XANA's puppet has managed to breach Willis's defense and is about to hit him with an electrified punch, his possession of her ends due to the effects of the virus causing the Mountain Replika inside the dam computer to fall apart. Eva falls unconcious and, after everyone's had a moment of relief, they later greet Eva when she wakes up. Eva is skeptical of the strange boy and his two partners, as well as their story about XANA, but Pulsemon acts as character witness to back everything up. Spending time getting to know each other as they leave the dam behind, the two teens hit it off fairly easily. Eva teases Willis over his chosen nickname, saying she thinks his real name of Wallace sounds better. The pair part on good terms, exchanging e-mails in the process.

Back at Kadic with the Lyoko Warriors who, after an oral quiz in Mrs. Hertz's class with a tense tied lead between Jeremy and Laura, meet up after class to discuss their recent couple of successful Replika missions as Jeremy relays the report from Willis on his own recent success. Ulrich, however, notes an intutiton he's been having that Laura may have been trying to spy on them over the past several days. The group agrees they should be more careful sneaking off to the factory. Laura continues to try deducing where they keep sneaking off to and grows increasingly frustrated as she can figure out the general areas they vanish at but can never pinpoint the exact vanishing point. When the current A-plot at one point prompts Jeremy to return to the dorms to grab a CD with important data, Laura sulking in the forest catches him popping up seemingly out of nowhere and checks the clearing he came out of. When she initially spots nothing, she falls back on the ground and hits her head on something metal hidden by the grass. She recognizes that a manhole to a storm sewer is a weird thing to have in the middle of the park and decides to investigate, ducking into one of the side tunnels when she hears Jeremy returning and then silently following behind as he returns to the factory. She hides in the nook of the factory boiler room above the lab and witnesses the Lyoko Warriors, human and Digimon alike, discussing matters she doesn't have the full picture to understand. Once everybody leaves, she climbs down to examine the interface. And after some poking around its files, she discovers a series of files that begins with the sentence, "Dairy of Jeremy Belpois, Kadic Academy, 8th grade student, October 9th." This episode ends on one intrugued Laura.

Another episode starts in Odaiba, Tokyo and focuses first on a girl named Noriko Kawada and her Digimon partner, a Bearmon. Noriko proudly explains the extra credit project she has been working on for her advanced classes, after which Bearmon reminds her that play is just as important as work for a growing kid. With some convincing, and to Bearmon's delight, Norkio agrees to a break to go out with him for a quick game of catch. However, when the pair are out and tossing the ball around, a nearby streetlight emits black smoke the trails down and targets Noriko. Bearmon notices only too late to warn her, and he can only watch in horror as the smoke painfully injects itself into her from behind. Noriko screams before dropping limp to the ground. Then she slowly gets up and scowls, a sinister sigil glowing in her eyes.

Back in the French side of things, following a scene of breakfast shenanigans, Jeremy gets an urgent text from Izzy that he and the other Lyoko Warriors join him on video call as soon as they can. At the factory, Izzy explains the situation: several of the younger DigiDestined in Odaiba had wandered from home without a word. And all of their partners described seeing the same phenomena in their kids before losing them. Animalistic aggression, sudden superhuman feats, a growling voice, and a certain sigil glowing in their eyes. All signs of Xanafication. As William points out, DigiDestined are supposed to be immune to XANA's control, which Izzy admits is the part that troubles him the most. When Jeremy asks if the known XANA victims had any common thread that might start to explain his ability to control them, Izzy reluctantly brings up the dark spores and tells the story of how Ken Ichijouji, the victim of the original Dark Spore, had been kidnapped and his spore imperfectly copied to a group of twenty children who had been led to believe it would improve their lives. But while the spores did improve their physical health and intellect, it also corrupted them, making them colder and more ruthless. The spore copies could not be removed, but the negative effects could be negated by unconditional love and friendship; to that end, the twenty became DigiDestined and were given their own loving partners. Aelita speculates that if the Dark Spores are still there, XANA may be using them as a back door into their minds. The Lyoko Warriors agree to come to Odaiba via Digi-Port to track down the kids, figure out what XANA is doing with them, and free them from his control.

Mainly through the assistance of flying Digimon for aerial view (such as Biyomon, Tentomon, Patamon, and Hawkmon, joined by Munin), the Xanafied Dark Spore children are spotted moving about an abandoened factory on the edge of the island, assembling something. The assembled Japanese DigiDestined and Lyoko Warriors easily deduce that the factory's main control computer had been linked to one of XANA's Replikas in the Digital World, but the supercomputer is heavily fortified by XANA's forces. Izzy, able to log into the computer with enough access to spot the activated Tower and establish a Digi-Port in the one closest to it but not enough to breach the core drive and implement the virus, decides a team of Lyoko Warriors should enter the Replika through the Port and deactive the Tower controlling the Dark Spore children while the rest handle things in the real world. Aelita, Ulrich, and Odd go to the Replika. Jeremy stays with Izzy, while Yumi and William go with the others to investigate XANA's actions on Earth. William had previously learned to speak Japanese to impress Yumi, which the latter claims technically did work, just not enough to change her mind about not daing him. They are accompanied by a younger Dark Spore child who had thus far seemingly managed to evade control by XANA, a little boy barely older than Hiroki named Takashi Yoshizawa.

Team Replika find themselves in another copy of the Mountain Sector and quickly run into XANA's usual welcoming committee. As they fight through XANA's monsters, the Scythozoa pulls a sneak attack and possesses Aelita to get her to try and sacrifice herself in another bid to draw out Franz Hopper. Ulrich and Odd are forced to delay deactivating the Tower to try drawing the possessed Aelita back to the Digi-Port and back to Earth where XANA's control would be cut. On Earth, Team Factory infiltrates the possessed Dark Spore children's workspace to get a look at what they're doing and send images back, taking note of an active computer terminal with a closed Digi-Port. Yumi mentions the cybernetic spiders they found in the Amazon during their first Replika mission. Meanwhile, the two DigiDestined groups' respective smart guys deduce that the objects being built are the components for relay antennas, possibly for the robot army XANA seems to have been building. Unfortunately, one Xanafied kid spots the infiltration group, and the entire army is surrounding them. Fighting ensues, and Yumi notices frightened little Takashi is sucked into the middle of it. In order to get him to safety, Yumi opens the Digi-Port on the terminal with her D-3 but then hears Takashi say in a demonic voice, "By your orders, XANA," realizing she'd been played just in time to get kicked across the room.

With the Port open, a select team of possessed kids begin carrying completed relay antenna parts through to the Digital World while the rest prevent any heroes from interfering. In the Mountain Replika, Odd and Ulrich struggle to do what they can to break XANA's control of Aelita, but she ends up running off to the edge of the Replika where the inside of the Virtual Shell gate comes into view. Jeremy informs them of the situation on Earth, so Odd tells Ulrich to go deal with the Tower while he follows Aelita. Outside, Odd discovers that the Virtual Shell of this Mountain Sector is built atop the peak of Infinity Mountain, the biggest mountain in the Digital World and incidentally the center of File Island. XANA must've been taking advantage of the altitude and the clouds surrounding the upper mountain to mask this Replika from Jeremy's scans, he suspects. As the Xanafied children in the Digital World carry the parts to a cave off in the upper corner of the mountain, Ulrich Super Sprints into the Tower and deactivates it, allowing the heroes on Earth to make it through. Yumi quickly runs to help Odd deal with Aelita while the local DigiDestined go after the other possessed. Yumi and Odd are able to lure Aelita through the Digi-Port outside of the Replika Shell, but XANA simply releases control of the Dark Spore children in the Digital World after raising a firewall around the gathered machine parts.

After making sure Ulrich has left the Mountain Replika first, Izzy finally approaches the factory computer and is able to inject the Replika-destorying virus, and everyone outside of it watches its Virtual Shell implode. The DigiDestined of Odaiba thank the Lyoko Warriors for their help in rescuing the possessed, but concerns still linger over what XANA plans to do with those relay antennae.

Another episode starts with the Lyoko Warriors on another quest to the Cortex in the hopes of searching its databanks for information on Anthea's involvement. For the first act of the episode, the mission goes fairly well, even when the Ninjas get involved. Unfortunately for the heroes, they realize only too late that they're being corralled into one corner of the core room when an energy field encompasses and traps them. Losing all contact with his friends, Jeremy realizes there's only one option left and calls Shelley back to the lab to mon the supercomputer and virtualize in the only one left to save them now. To Shelley's initial shock, Jeremy is, in fact, referring to himself, and Shelley virtualizes him straight to the Cortex. Given an Overwing and real-time warnings of landscape shifts by Shelley, Jeremy makes his way to the core room. He finds the other Warriors' prison fairly quickly and moves to try hacking it open, ignoring the Peter Pan jokes from some of his friends over his elf-like appearance in the Digital World. The Ninjas arrive, but Jeremy just barely manages to dodge multiple assaults before resorting to use of a Teleportation power, which he had previously given his own avatar upon bug fixes after Odd turned it down.

After a bit of cat-and-mouse with the Ninjas gives Jeremy enough time to decode the barrier holding his friends, the rest of the gang jump in to fight the Ninjas off before all make a break out of the core chamber. But Jeremy starts to realize something is very wrong when he calls to Shelley to energize the others into the waiting MegaPod and gets radio silence. He requests that one of the others devirtualize him so that he can check the lab, to which Odd quickly obliges. Arriving back at the factory, Jeremy quickly climbs the ladder to the lab where he finds Shelley knocked out cold, access to and from the cyberspace room locked, and an open data line between the supercomputer and another: the Cortex's. Tyron appears on video chat as Jeremy examines the line and gleefully mocks him for playing right into his plans; Tyron needed all the Lyoko Warriors preoccupied in "what [they] call the Cortex," to which Jeremy realizes gave an unseen agent of his the opportunity to slip in and steal data from Hopper's supercomputer. Once their conversation ends, Tyron ends the chat while severing the data link between their supercomputers. Jeremy brings everyone back while bitterly informing them that Tyron has played them all. Outside, Laura in a stealth suit hikes back towards Kadic as Tyron congratulates her over the phone.

The next time a team of Lyoko Warriors visits the Cortex, they find it drastically changed. Not only is the build of the virtual landscape entirely stable now, but the building block look has been reconfigured to look like clusters of pseudo buildings with small forests between. There is a ring of sand around the outer edge, a ring of ice water surrounding the core chamber, and the satellite "landmasses" surrounding the main disc-shaped landscape have mountain peaks jutting out of them. Furthermore, Jeremy notes that several new Towers have been added to the layout scattered throughout. Overall, the Cotex has completely changed from looking like an abandoned industrial site to a small city, with the core chamber looming in the center like a dome-shaped black castle. The trip from the edge to the core chamber is actually a lot smoother now that the landmass is no longer constantly reconfiguring itself. As Aelita accesses the interface in the core chamber to try and assess any new resources added to the Cortex supercomputer hard drive for what all had been copied directly from Lyoko's, she again spots Anthea via webcam in the lab. But just as she's barely begun to successfully make contact, the Ninjas interfere and force a retreat.

After the team has returned, Jeremy notes something on Aelita's mind and talks to her in private. She wants to use the Skid and the translation program to infiltrate Deckard Inc and find her mother. Jeremy is concerned for multiple reasons, including the fact that Deckard Inc is still a very much active facility, but Aelita is confident it could be pulled off if they play their cards right. The now stable state of the Cortex means it is safe to bring the Skid in to dock on one of its Towers, the others can stay to guard the Skid should it be targeted in the Digital World, and a simple study of the facility's schedule should allow one small infiltrator to slip by any unwanted attention. Aelita also brings up the fact that she hadn't seen her mother since the raid of their mountain cottage when she was a toddler, and they still don't know how Anthea went from being a captive of Project Carthage to working at Tyron's facility. She's missed her mother sorely and has had nightmares about the day she lost her; nightmares even Munin couldn't quell. Recognizing just how much this means to Aelita, Jeremy agrees to start preparing for the mission. The two have a tender moment together (during which Jeremy calls Aelita "o angel of mine" and Aelita calls Jeremy "my proxy-pie"), which is comically cut short when the two catch Munin and Shelley spying on them, and the Digimon clumsily excuse themselves from the scene.

Within a day or so, Jeremy manages to acquire both the floor plan and schedule for the Deckard Inc facility thanks to Walter Stern's business connections. The gang set off for the Cortex, where Jeremy guides Aelita in docking the Skid to a Tower in a forest-like area in the outer rim. The others on the mission stay to guard the sub while Aelita is translated into enemy territory and Solid Snakes herself to the lab undetected. Once she sees her mother alone there, she quietly steps forward to reveal herself and then recalls a few faint childhood memories to confirm to the shocked Anthea she is who she appears to be. After Aelita explains how she is manifesting herself to Anthea as a digital spectre, the two cherish the joyful opportunity to catch up. Aelita learns that Project Carthage had allegedly reported her and her father dead after they failed to capture them in 1994, and Anthea learns that Franz is permanently virtualized and lost somewhere in the net but still alive.

Then Tyron reveals he's been listening in the whole time and shows that his interface alerted him to their arrival with a superscan and an updated virtual map taken from codes copied from Franz's supercomputer. Aelita immediately demands an explanation of how Tyron got her mother in his lab working for him when she last saw her being kidnapped, to which Anthea is quick to explain that Lowell Tyron had saved her from Project Carthage captivity and both had decided to continue the presumed-late Waldo Schaeffer to honor his memory. Aelita's translation time limit starts to run out before she can get any further clarification, but Anthea reassures her that they can still always be together in spirit through her and Waldo's old matching pendants before her daughter's spectre form dissipates. The episode ends with the Lyoko Warriors regrouping to ponder this new information.

More stuff. Including the full return of Franz Hopper (with Jeremy and possibly Anthea's help), a confrontation between him and Tyron, the Lyoko Warriors figuring out Laura is the spy at Kadic, likely more interactions with the DigiDestined and their partners in Japan, and then finally a big climactic moment of Dark Gennai revealing himself to be the one Franz, Anthea, and Tyron knew as Mark Hollenback and that he allowed Tyron to "rescue" Anthea while planting his own agents as moles in Tyron's ranks. And then the arc comes to some sort of conclusion after Dark Gennai/Hollenback has robbed Tyron of his resources.

End of Arc Two.