The MoonScoop Group announced a sequel series titled Code Lyoko: Evolution that ran for one season and consisted of 26 episodes.
The series revolves around a gang of boarding-school students who travel to the virtual world of Lyoko, within a quantum supercomputer, to battle XANA, a malevolent AI/multi-agent system who desires to rule all of humanity.
When Milly tells her teddy bear that she wishes she were bigger and leaves it in the garden shed, XANA possesses it and uses it to attack those who make fun of her.
Odd and Ulrich must free Aelita and deactivate the tower before Yumi is defeated by the possessed samurai armor and Jeremy is taken away by the police.
On top of that, they learn that XANA is responsible for the damage being caused to the school by using ultrasonic sound waves, which continues to get worse.
Jeremy has to fix the damage he caused in time to save Odd, who ends up trapped inside the school with Milly, Tamiya, and Kiwi.
Unfortunately, after two tries, both ending in failure, Aelita, with the help of Yumi and Ulrich, has to deactivate the tower or else Odd, Milly, Tamiya, and Kiwi will be killed.
He also develops a new tower-scanning program that instantly detects activated towers, allowing Aelita to live on Earth.
In order to compensate for William, who is still under XANA's control, Jeremy sets to work designing brand-new virtual attire and digital "enhanced" weaponry and abilities for his friends and recreating the rest of Lyoko.
While Jeremy's clone is impressing Jim outside, William appears on Lyoko and tries to put the tower under his master's control.
While Odd holds the Jeremy clone off, Aelita, Yumi, and Ulrich go to Lyoko with new outfits and somewhat much stronger abilities and slight improvements of their old weapons.
Jim's nephew, Chris, the drummer of the Subdigitals, pays a visit to Kadic to look for an opening act for the band's next concert.
The new virtual, submersible "submarine" (as Jeremy calls it) is almost complete, the last step being a secondary program that needs to be run by 4 PM the next day.
When a comet passes near Earth, XANA uses a laser-equipped military satellite to split it into chunks, simultaneously aiming the bulk of it directly at the factory.
Aelita, Odd, and Ulrich are exploring the digital sea at the time, and XANA traps them with a firewall to prevent them from stopping the attack.
Jeremy, Aelita, Ulrich, and Odd go with the rest of their science class on a field trip to an island in the middle of a nearby lake to study water-based plant life.
Though XANA soon manages to regain control of William, Yumi is saved by Aelita, who escaped the island on Sissi's bike.
Jeremy has finally perfected his "teleportation" process, allowing him to send his four best friends to the location of XANA's supercomputer in the real world to destroy it and leave no trace of their heroic activities.
Before they can stop him, however, William manages to sever their connection to the real world, bringing them back to Lyoko in the middle of their mission.
A bug in his virtual avatar spreads to Yumi and Aelita, causing annoying pauses and random devirtualization in the Desert Replika.
Meanwhile, at the site of the Replika's supercomputer, XANA materializes Kankrelats in the real world to stop Ulrich and Yumi.
Despite the bug, their mission to destroy XANA's next Replika ends in success, this time by Ulrich, and Odd's luck returns soon afterwards.
While there, she messes with the computer despite Odd's pleas not to, creating a glitch in a program Jeremy is installing that causes every virtualization to happen in the wrong sector and prevents materialization.
As Brynja has not been told anything about the purpose of the Supercomputer, nor does it appear that she even cared in the first place, they have no need to perform a return trip to the past before she leaves.
Meanwhile, Odd, in an attempt to impress a girl in photography class, inadvertently sends the photo to Sissi, who in turn shows it to her father.
However, XANA draws on the power of his many Replikas to create a new monster: the "Kolossus," a massive creature resembling a fire elemental with a sword for a hand.
In order to defeat XANA, whom they have vastly underestimated, Jeremy plans to design another multi-agent system to combat him.
In more immediate matters, Jeremy has figured out how to free William from XANA, but needs to run his program directly from the Ice Replika's supercomputer.
However, XANA is not willing to give up without a fight, activating a tower to possess William once again while sending the Kolossus to deal with Franz.
When it comes time to shut down the Supercomputer, all but Yumi are unwilling to go through with it: Aelita is still holding onto the hope that her father can somehow be saved, Jeremy does not want to take away the thing which made them friends, and Odd and Ulrich both liked being heroes.