Four ordinary high school students, Jeremie Belpois, Odd Della Robbia, Ulrich Stern, and Yumi Ishiyama, must help a virtual humanoid named Aelita to stop the evil artificial intelligence XANA from attacking Earth by traveling to the virtual world, Lyoko.

The last chapter in the game features a glimpse of the third season's premiere episode, but with a lot of changes.

The game features both side-scrolling and 3D gameplay, reflecting the two animation styles of the series.

In the real world, side-scrolling gameplay is used, resembling that used in traditional role-playing games.

On Lyoko, gameplay consists of third-person fighting, utilizing the special abilities of each character to defeat monsters and solve puzzles.