Code Lyoko is about a group of five boarding school students enrolled at Kadic Junior High School: Aelita Schaeffer, Jeremy Belpois, Odd Della Robbia, Ulrich Stern, and Yumi Ishiyama. The students travel to the virtual world of Lyoko — which is found in a supercomputer housed in the basement of an abandoned factory near the school — to fight against a deadly multi-agent system named Xana.

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. Xana is also able to attack the real world by activating towers on Lyoko, which act as links to the real world. When these towers are activated, Xana is able to seize control of other computers and electrical systems as well as occasionally possessing organic life-forms or generating copies of them. Aelita must get to the activated tower(s) out of the 41 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, (going back in time cannot bring back the dead), and deal with the many clashes of personality at the same time. 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. However, as a downside, returning to the past adds a qubit to the supercomputer, doubling its power and therefore Xana's with each use.

The five-minute pilot of Code Lyoko, titled Garage Kids, was released in 2001. Though similar in concept, it differs in execution, such as the protagonists possessing their powers in the real world, and some characters not having appearances, such as Sissi, Jim, and Aelita.