After a summer vacation, the group is still trying to find a way to fight XANA. Meanwhile, XANA is trying to destroy Lyoko, which gives the group little to no time to look for a proper way to fight back. He does this by targeting the core of Lyoko, which contains the code that maintains the virtual world. In a side-story, Odd blackmails Jim into asking the principal to put him in the same classes as his friends. Also, Yumi decides against having a relationship with Ulrich, thinking it would be better if they were just friends.
Yumi, while on a field trip with hr 10th grade class, finds herself up against the students, teachers, and even the bus driver, all of whom XANA has possessed. At the same time, XANA had decided that simply attacking the core to get rid of Lyoko would be a hassle, and plans to get rid of it through an alternate means: destroying the sectors one at a time. And so, he uses the Scyphozoa to possess Aelita and enter a new code, XANA, into the forest sector's way tower, which in turn deleted the entire forest. In a side-story, Jeremie, Odd and Hervé compete for class ...
The team is attacked by a large amount of food possessed by XANA. At the same time, he tries to prevent access to the Mountain sector's activated tower by submerging it in the digital sea, but Odd and Aelita go to Carthage to stop him. During which, XANA also attacks Lyoko's core.
Xana hacks into a weapons manufacturing computer network, and leaves a paper trail pointing to Jeremie! Soon, government agents arrive at the school looking for him. When they end up tracking Jeremie to the factory, Xana possesses them to lead an attack on the supercomputer itself!
Aelita gets mad at Jeremie, so she and Odd go into Lyoko without telling anybody, which causes problems. Xana had created a diversion to get everybody to deactivate the tower in the mountain sector while the monsters worked on destroying the heart of Lyoko. Jeremie and Aelita find a strand of DNA that belongs to Franz Hopper, indicating he may be still alive.
Yumi's classmate Johnny has a crush on her and won't let her out of his site, making it hard to help her friends battle the swarm of birds XANA sent to attack them. When she gets hurt the warriors must go back in time in order to save her.
After an angry Yumi chastises and rejects him, a bitter William sets out to uncover what she and her friends are hiding from the rest of the world. Unbeknownst to the gang who are preoccupied with an activated tower, a X.A.N.A. possessed demolitionist is placing a series of explosives through out the factory.
Ulrich and Odd return from a mission on Lyoko, but XANA has infected them with a virus causing them to believe they are seeing monsters in the real world. Jeremy knows how to help them, but XANA has launched another attack in Sector 5.
When XANA sabotages the supercomputer, weird bugs begin cropping up in Lyoko. With its power rapidly draining, Jeremie needs to repair it before it becomes completely useless. However, he seems to forget about boys' dorm inspection, so Jim forces him to stay behind. Meanwhile, XANA possesses vines to trip up the rest of the group, except Aelita. Since the attack keeps draining power from the supercomputer, with no other choice, Aelita purposefully wipes out the Ice Sector leaving only the Mountain Sector left.
During a test to materialize Ulrich directly into Sector 5, his mind and body become separated, leaving Ulrich's body trapped on Lyoko and his spirit stuck on Earth. What's worse, XANA possesses Ulrich's body and uses it to attack the core. Meanwhile, Suzanne, disappointed with Ulrich's bad grades, tries to place him in remedial classes.
With the loss of the virtual psychic ability and his recent less than stellar performances on Lyoko, Odd is in a major funk. To cheer him up, Jeremie decides to give his friend the power of teleportation. Everything seems to be going okay with the new ability until a bug in the program causes Odd to literally triplicate.
The students' grades are becoming affected by all the time they've spent fighting XANA, so they suggest adding William to the team, but Yumi is against it. However, the super computer's latest attack may be bad enough to change her mind.
With the destruction of Lyoko imminent and most of the gang preoccupied with personal matters, Aelita is forced to enter the virtual world with William, but will his misguided boldness and carelessness cost them everything that they have fought for?