Five months after the events of Code Lyoko: Evolution, the government is seeking to abolish the force responsible for the malevolent artificial intelligence (multi-agent system) X.A.N.A. After shutting down Project Carthage, the government decides to reopen this old sanction as a new task force named Eradication, in order to track down Lowell Tyron and find the creator of X.A.N.A.
As Lowell is known as Franz’s final associate, Tyron is recruited under special circumstances even though he abandoned Carthage and did his own research. The government then gives him funding to re-create the Cortex, and, by doing so, Tyron sets X.A.N.A. free once again. Tyron then creates a unstoppable tracing software in order to locate digital DNA to rematerialize Franz Hopper. Jeremy and his team, while continuing to search for Aelita’s long-lost mother, make a discovery that may finally annihilate X.A.N.A. for good, though it also leads them straight into the Men in Black. Caught in a battle between clashing forces, the Lyoko Warriors are now subject to being hunted by not only Tyron, but by the government as well.