The artificial intelligence known as Xana is obsessed with world domination. Towards that end, he has taken over the supercomputer in charge of the virtual world of Lyoko, which he largely dominates. Xana is also able to attack the real world by activating towers on Lyoko(usually one at a time), which act as links to the real world. When these towers are activated, Xana is able to seize control of other computers and epohalectrical systems as well as occasionally possessing organic life-forms or generating copies of them. The group has to get Aelita (The only one capable of de-activating towers) to the activated tower(s) out of the forty one scattered about Lyoko's four main regions to deactivate them, neutralizing Xana's attack on the real world.

Once the danger is averted, they can use the supercomputer to return to the past, leaving no one except themselves to remember any of the events that transpired. To complicate the situation, they must do this while ensuring their classmates and teachers are not killed (as going back in time cannot bring back the dead), and deal with the many clashes of personality at the same time. The time travel is programed by Jeremy using a time coordinate system (Which he usually limits to going back one day although there are exceptions) as Jeremy is the only one with the intelligence to understand the supercomputer's workings with the exception of Aelita who has to be on Lyoko to de-activate towers. The jump to the past takes back anyone who has been scanned in one of the scanners. Once back in time, they can use their knowledge of the future to alter events in their favor or the favor of others. This usually entails taking steps to keep one of Xana's attacks from taking place, though they do use the knowledge to prevent other unfavorable events that might not be related to Xana, such as the destruction of Jeremy's Kiwi 2 robot in "The Robots". However, as a downside, returning to the past adds a qubit to the supercomputer, doubling its power and therefore Xana's with each use.