In the fourth season, Lyoko is recreated, allowing the group to continue tracking Xana. Traveling into the digital sea in Jeremy's latest creation, a submersible ship called the Skidbladnir, the group finds a number of "Replikas", which are single-sector recreations of Lyoko. Each of these Replikas is controlled by another supercomputer, which is in turn controlled by Xana. To stop Xana once and for all, Jeremy devises a way to materialize his friends at the site of these supercomputers with their Lyoko abilities intact, giving them the necessary firepower to dismantle or to destroy them, all while continuing to battle the Xana-possessed William. The group has new outfits (in both Lyoko and the real world) and weapons to accompany the new season.

In the final few episodes of the season, the creation of a monster known as the Kolossus (which destroys the Skidbladnir) opens the gang to realize that with hundreds of supercomputers under his control, Xana cannot be defeated with Jeremy's teleportation method. To this end, Jeremy initiates a multi-agent program to destroy Xana and another program to free William. In "Fight to the Finish", Franz Hopper sacrifices himself to give this program enough power to destroy Xana and free William. In the epilogue, "Echoes", having completed their mission, the gang shuts down the supercomputer for good.