The second season, in contrast to the first, is much more plot-focused, though a decent portion of the episodes are still filler. The animation is more realistic and detailed, and Jim and Sissi's personalities have changed significantly, though some traces of their old personalities exist in some form. Aelita lives on Earth in the second season. In the first episode of the second season, she enrolls at Kadic under the name of Aelita Stones. She poses as a cousin of Odd, using a forged birth certificate created by Jeremy. Jeremy's new super scan program also means that Aelita doesn't need to stay on Lyoko to check for Xana's activity; however, due to her links to the supercomputer, Aelita will die if she runs out of Life Points on Lyoko and can only be devirtualized through one of the towers. Aelita also begins having visions of a life she supposedly never lived, and a man named Franz Hopper is shown to have connections to Lyoko. Also adding to the group's troubles is a new student named William Dunbar, who has begun to take an interest in Yumi.

Each member of the group now has vehicles to quickly transport them in Lyoko: Odd gets a hover skateboard called an "Overboard," Ulrich gets a one-wheeled motorcycle called an "Overbike," and Yumi gets a hover scooter called an "Overwing." Aelita can ride any vehicle by herself if necessary, but usually rides with another person. A fifth sector, Carthage, is discovered in Lyoko and turns out to be Xana's home sector, from which all of his data can be accessed, so the group goes on several journeys into this sector to do so. At the same time, Xana begins sending the Scyphozoa after Aelita to steal her memories, and has created three other new monsters, as well. The operations of the supercomputer are also somewhat demystified. Return trips are fewer (though still common) now, because it makes Xana stronger. Eventually, Xana's true purpose is revealed, as are the origins of the supercomputer, Lyoko, and Aelita herself. It is also discovered that the keys to Lyoko are within Aelita's memories, and Xana will be able to escape the supercomputer if it acquires them. In the end, despite the group's best efforts, Aelita's memories are stolen, apparently killing her, but Franz Hopper (revealed to be Aelita's father) revives her and restores her memory. However, Xana escapes the supercomputer, and the group, though unsure of how to do so, vows to continue fighting him.