During spring break, Odd Della Robbia discovers a Digivice and learns about the world of Digimon. His Digimon partner, conversely, learns of the Lyoko Warriors and the fight against XANA.

• Sector Five is recreated.
• Odd Della Robbia, Gumbo, Jeremy Belpois, Aelita "Stones", Ulrich Stern, Yumi Ishiyama, Jim Morales, Sissi Delmas, Herb Pichon, and Nicholas Poliakoff are introduced. William Dunbar, XANA, and Franz Hopper are indirectly introduced by backstory exposition.

Merely a day after Jeremy and Aelita have completed the first step in recreating Lyoko, a once lost Lyoko Warrior seemingly returns unscathed. But not all is as it seems. Meanwhile, Odd is in hot water with his phys ed teacher over a viral video.

• William Dunbar, XANA, Leon, and Shelley (unnamed) are introduced.
• The Lyoko Warriors are first virtualized within this series, and the rebuilt Sector Five is formally introduced.
• Leon digivolves from a Tsunomon to an Elecmon and later gets his nickname from Odd.

Jeremy has become irritable as of late due to overloading himself with work, and his new partner tries to get him to give himself a break. To that end, Jeremy programs a digital clone of himself to handle school, but things naturally go sideways.

• The Ice Sector is recreated.
• Suzanne Hertz is introduced.
• A Tower is first activated in this episode, and Jeremy and Aelita reveal to the other Lyoko Warriors that they were able to implant the Annex Program into them from Franz Hopper's e-mail, allowing them to deactivate Towers same as Aelita. This time, Yumi deactivates the Tower.
• Shelley digivolves from a Chapmon to a Kamemon and gets his nickname from Odd.

Jeremy and Shelley discuss means of exploring the Digital World beyond Lyoko and how to safely navigate the Digital Sea. Meanwhile, Aelita is accepted for a musical audition, but her celebration is cut.

• The Desert Sector is recreated.
• Chris Morales of the Subdigitals is introduced. Yumi's Digimon (type, and subsequently nickname, pending) is also introduced.
• XANA can create polymorphic spectres of Digimon that can copy the original's abilities if a previous spectre has come in contact with the original.
• Odd deactivates his first Tower.
• Jeremy agrees to reach out to Izzy Izumi to fill the other DigiDestined in on the fight against XANA.

After a string of email correspondence with Jeremy, Izzy and Tentomon arrive in town to see the supercomputer for themselves. Unfortunately, XANA and William both cause trouble.

• The Forest Sector is recreated.
• Izzy Izumi, Tentomon, and Michel Takaishi are introduced.
• XANA possesses a human being for the first time in this series this episode: Michel Takaishi.
• Izzy gifts Jeremy the Digi-Tablet and the code to build a Cyberspace Room for the Lyoko Digimon within the supercomputer's drives. Aelita also receives her Digivice and her partner's egg.

Jeremy shuts off the supercomputer interface to install some hardware modifications sent by Izzy, but not before putting the Towers of Lyoko on temporary lockdown. The Digimon stay on Lyoko to keep an eye on things, just in case.

• The Mountain Sector is recreated, completing Lyoko's recreation.
• Aelita's Digimon partner is introduced, still at Fresh level and not yet nicknamed.
• The supercomputer is given a proper Digivice port and two USB ports.
• XANA-William gets devirtualized for the first time this series.

Jeremy, Aelita, and Shelley have just about finished creating a submarine that can help the Lyoko Warriors travel beyond the Digital Sea. Unfortunately, their new sub has become a target for XANA while the kids are at school.

• The Skidbladnir is created, named by Aelita's old childhood book, Viking Gods and Legends by Andrea Hopkins.
• Aelita's Digimon has since digivolved into a Tapirmon, and they're nicknamed Munin, also by Viking Gods and Legends.

The Lyoko Warriors decide to take their new digital submarine out for a test drive. But a buggy navigational system lands the team in hot water.

• The Skidbladnir launches for the first time, marking the first time the Lyoko Warriors traverse the Digital Sea.

While the Lyoko Warriors begin scoping out the world beyond the Digital Sea for the first Replika to target, Ulrich finds himself caught up in the drama of a small village being harassed for protection money.

• The Lyoko Warriors begin exploring the greater Digital World.
• It's discovered that humans virtualized via the scanners are unable to exit the Digital World through traditional Digi-Ports. Jeremy resolves to figure out a workaround.

A bug in the supercomputer interferes with Gumbo's reconfiguration, causing him instead to fall out of a scanner in flesh and blood. It's a race against the clock to fix the bug and return him to a digital state.

• Multiple events of Code Lyoko past are referenced, including Odd and Yumi switching bodies ("A Fine Mess"), Odd's accidental cloning into three due to a bugged teleporting power ("Triple Trouble"), and Ulrich's mind and body being separated while testing an experimental transfer protocol ("Nobody in Particular").
• The teleportation power Jeremy created for Odd in "Triple Trouble", fixed of its bug, is revealed to still exist, allegedly attached to an "unused asset" in the supercomputer.

When Jeremy finally tracks down the Tower XANA controls William with, the heroes set off on a mission to liberate him that takes them to a strange Cortex-shaped Replika like nothing they'd seen before.

• The Cortex and the Kolossus are introduced.
• Franz Hopper's presumed connection to the Cortex is teased.
• William is freed from XANA's control and resumes life at Kadic.
• The Skidbladnir and the Lyoko Digimon are lost at sea.

The Digimon of Lyoko are recovered at File Island. But what starts off as a simple submarine repair in Factorial Town quickly becomes a race against time when XANA's forces stop by.

• The Skidbladnir is recovered and ultimately restored to working condition.
• File Island, Whamon, Joe Kido, Gomamon/Ikkakumon, Tai Kamiya, Agumon/Greymon, and the Pagumon that becomes William's partner are introduced.
• Tentomon's Champion form, Kabuterimon, is introduced.
• Leon recovers past memories of his alliance with Tai and his friends and digivolves into Leomon, becoming the first Lyoko Digimon to reach Champion level within the series.
• The Kolossus is killed for the first time.
• William rejoins the Lyoko Warriors and receives his own Digivice and Digimon partner.