Jeremy Belpois, a 12-year-old prodigy attending boarding school at Kadic Academy, discovers a quantum supercomputer in an abandoned factory near his school. Upon activating it, he discovers a virtual world called Lyoko with an artificially intelligent girl named Aelita trapped inside it. Jeremy learns of X.A.N.A., a fully autonomous, malevolent, and highly intelligent multi-agent system, that also dwells within the Supercomputer. Using Lyoko's powers, X.A.N.A can possess electronics and objects in the real world like a virus to wreak havoc. X.A.N.A.'s primary objective is to eliminate anyone aware of the Supercomputer's existence so that it will be free to conquer the real world and destroy all humanity.

Jeremy and Aelita construct a digital submarine, the Skidbladnir, to travel across the Digital Sea to destroy X.A.N.A.'s "Replikas," which are copies of Lyoko's sectors that are linked to X.A.N.A.-controlled supercomputers on Earth, all created for its goal of world domination. X.A.N.A. uses William as its general throughout the season to defend the Replikas and target the Lyoko Warriors in any way he can. To prevent suspicion regarding William's disappearance, Jeremy manages to program a spectre to take William's place at Kadic, although the clone has low-level intelligence and acts very stupid. Near the end of the season, X.A.N.A. decides to draw energy from all of its Replikas to create the Kolossus, a gigantic monster that later destroys the Skidbladnir. Before it is destroyed, Jeremy frees William from X.A.N.A.'s control. After his return, he has a difficult time gaining the trust of the group. While Ulrich defeats the Kolossus, Franz Hopper sacrifices himself to power Jeremy's "anti-X.A.N.A. program," which destroys X.A.N.A. forever upon activation. Shortly after, the group, albeit reluctant due to their nostalgia, decides to shut down the Supercomputer.