A student named Milly seeks the comfort of her teddy bear after being embarrassed and ostracized due to her young age by Sissi, the school's bully/diva. Milly believes that her teddy is the only one that she can turn to for comfort and support. A corrupted super computer known as X.A.N.A. enters the real world by possessing the bear. In a quest to strike and destroy his enemies, the X.A.N.A infected teddy bear increases to an enormous size. No one is safe as this monstrosity creates a path of destruction.

During the school physicals, Xana possesses the school nurse, Yolande, and has her kidnap Aelita. The rest of the group beats her to the factory, but has no way to get Aelita from the far more powerful nurse. Having no other choice, Jeremie decides to test out an experiment which will give a person the same powers as one possessed by Xana. To do this, he has to activate a tower like Xana. Jeremie's towers turn green instead of red. Odd volunteers, and is enhanced by a ghost of Jeremie's design. This allows Odd to fight the nurse effectively while the others deactivate the tower. This fortune doesn't last, however. Xana is able to take over Jeremie's tower, reversing the effect of the ghost to drain Odd's energy. And on Lyoko, Xana makes everything invisible. Now the group has to deactivate not only the original tower, but the tower that's draining Odd's energy.

When the school holds a concert in the gym, William accidentally drops a mixing board for the DJ contest. Odd offers to fix it, and tries to get Jeremie to help. Jeremie is busy, so Aelita offers her help. She easily fixes the device, and finds that she is quite talented in using it. The school is holding its finals, as well, and Odd finds that he is not prepared in the least. Meanwhile, Xana possesses Jim and takes Aelita to the factory in order to deliver her to the Scyphozoa.

When Ulrich learns that Yumi might have to go back to Japan because her father lost his job, he can't accept losing her. After hearing the lottery numbers on the radio though, he gets an idea. Using a return trip, he is able to get a ticket with the winning numbers and give it to Mr. and Mrs. Ishiyama. When the others find out, they kick him out of the group until they can figure out what to do. To make matters worse, Xana activates a tower and possesses Nicolas. On top of that, he creates an army of Krabs to guard it.

After a malfunction and a little bug with the regular materialization program, Odd and Yumi are bugged up, ending up in each others' bodies. Even worse, their atoms start splitting after a while due to being dematerialized, even on Lyoko. The gang has to go to Lyoko and fix the problem before Odd and Yumi disintegrate and disappear forever, but it's not easy when Xana tries to stop them.

After a trip to the Carthage Region, Jeremie believes he has the data necessary to cure Aelita's virus. While the two work on the cure, Odd, Ulrich, and Yumi go to a rock climbing contest. Odd races against Hervé, who is no match for Odd. William then goads Ulrich into racing, despite his obvious reluctance. During the race, Ulrich gets dizzy and falls. Yumi realizes that he must have vertigo. Ulrich, embarrassed, runs off. Meanwhile, Jeremie finds the anti-virus and gives it to Aelita. Despite some problem with the application, it seems to work. However, this does not last. An error in the anti-virus causes her to turn invisible. On top of that, she can't enter the towers on Lyoko, making it impossible for her to stop Xana's latest attack, which is a possessed pack of wolves targeting Odd, Ulrich, and Yumi.

Aelita's visions become a problem once again, but not the same visions as before. This time, she has visions of her and Franz Hopper being chased by government agents. The visions come even when she's awake, causing her to lose consciousness while at the pool. Wanting to know the source of the visions, she heads to the Hermitage to learn more about them. Jeremie discovers that Xana is causing the visions through her link to the supercomputer. During the mission to stop them, Aelita breaks away and heads to The Carthage Region, determined to discover the source of the visions.

After reading about a dead man named Leon Corbe, who died during the construction of Kadic, Sissi decides to hold a séance to communicate with him. She manages to convince Ulrich to attend. During the séance, one of Xana's ghosts appears in the form of a four-armed monster. At first, it seem docile, but quickly gets angry and attacks. Ulrich leaves Sissi with Odd while he goes to tell Jeremie. Jeremie can't find an activated tower, which seems wrong considering the situation. As Jim patrols the hallways, he is picked up by an invisible object. Jeremie, Odd, and Ulrich arrive to spray it with a fire extinguisher, confirming that it's a ghost and implying that the super scan is broken. With the ghost on the loose, the group heads off to the factory. After they arrive, Aelita, Odd, and Yumi head to Lyoko. Odd looks for the tower while the other two head to The Carthage Region to fix the super scan. Meanwhile, Jeremie and Ulrich are left to deal with the ghost.

During a mission to The Carthage Region, the Scyphozoa attacks Yumi, stealing her human DNA, having her trapped on Lyoko. To make matters worse, it's picture day for her class and she will be suspended if absent. After some discussion, Ulrich gets the idea to have Sissi stand in for Yumi. Strangely, Sissi agrees and asks for nothing in return. During this, Jeremie tries to come up with a way to bring Yumi back. Aelita thinks of a way, but won't tell Jeremie about it. She only tells him once she gets to Lyoko, so he can't object. She begins to transfer her own genetic code to Yumi, which will let Xana take her memory at will, being exposed. Luckily, Odd and Ulrich get there in time to stop her. Meanwhile, Jermie figures out that Yumi's DNA should be stored in XANA's memory, which is accessible through Sector Five.

It's Saint Valentine's Day and love is in the air. Ulrich forgets, so at last minute writes a poem for Yumi. However, when William presents Yumi with flowers, Ulrich gets jealous and reads the poem to Sissi instead, hoping to elicit jealousy from Yumi. The two end up in a fight, both bothered and wondering if the other really likes them. Also, a man possessed by Xana leaves a necklace at Aelita's door, Aelita is convinced that it was Jeremie who got it for her. Since Jeremie didn't actually get it, he's left to wonder who did, and ends up suspecting Odd, who avoids the question. This puts the two at odds, so to speak. Meanwhile, Aelita's necklace takes control of her and forces her to deliver herself to the Scyphozoa. Luckily, Odd arrives in time, and is able to save Aelita from the Scyphozoa by "threatening" to kill her.

After a Xana attack, Jeremie insists on a return trip, regardless of the fact that Xana didn't even cause any damage. When questioned, he gets defensive and angry, insisting that it's necessary. Further questioning on the matter leads to the same result. After the next return trip, Jeremie is found unconscious in his room. Yumi and Ulrich go searching through Jeremie's room to see what they can find about Jeremie's problem. Upon decoding a video diary that is stored on his computer, they learn that he had been using the return trips to increase his own intelligence. When he's about to be taken to the hospital, Xana attacks, possessing the ambulance and driving it towards the river with Yumi with him. Now the others have to save Jeremie and deactivate the tower without Jeremie's help.

Xana creates a ghost called a polymorphic specter, that can change its shape or form at will and doesn't need to possess a host, then uses it to drive a wedge between the group by having it kiss people while disguised as them. At the end of the episode Aelita kisses Jeremy to see how he'll react. He (predictably) freezes up.

During a short film made by Odd and starring Sissi, Sissi seems to be possessed by a ghost. She does not act as expected, however. Instead, she starts speaking in some strange language, focusing on Jeremie as she does. She is taken to the infirmary as a result. Later on, she walks into Jeremie's room and writes some code on a piece of paper. Jeremie translates the code, revealing a message stating a desire to help. Sissi is sent to the hospital after this, forcing Odd and Yumi to go there and collect her. On a trip to Lyoko, Aelita and Ulrich discover a white tower. Xana isn't happy about the tower, and sends Megatanks to shut it down forcibly. At the same time, it activates a tower and possesses a nurse at the hospital to do the same to Sissi. Odd and Yumi are able to prevent the nurse from doing so. They bring Sissi to the factory to finish the message she started earlier. She manages to type most of it out before Xana succeeds in shutting down the white tower. After Xana's tower is shut down, Jeremie translates the message, revealing that Franz Hopper had activated the white tower.

When Aelita's dreams and hallucinations become too disruptive to ignore, the group heads to the Hermitage to discover their source. There, Aelita finds a doll she inexplicably recognizes to be Mister Pück. Hidden on this doll is a key to a train station locker, which contains the heavily encrypted diary of Franz Hopper. Upon its discovery, Xana takes action, possessing Jeremie, to ensure they'll never be able to read it. When they deactivate the tower and Jeremie comes to his senses, Yumi explains to Jeremie why Xana can possess him and not Ulrich, Aelita, Odd, or Yumi.

After Xana possesses the principal of the school and kidnaps Odd and Yumi, he gives Jeremie an ultimatum: deliver Aelita to the Scyphozoa or sacrifice Odd and Yumi. However, Jeremie and Aelita go to Sissi for help and Sissi agrees to be tempoarily part of the group to help save her father and eradicate Xana.

Jeremy is woken up to an alarm signal, with no activated towers, so he goes back to sleep. The next morning, while Jeremy and Aelita are investigating Jeremy's computer, Odd looks for his DVD of his movie "I Guess Our Guest is a Ghost" to show the famous news reporter T.V. (Thomas Vincint), who is coming to the school to do a report on the lackluster of today's schools. Later, another tower is activated and Odd, Ulrich and Aelita are sent to Lyoko, only for the tower to deactivate itself. Then another tower activates and deactivates. Jeremy and Aelita stay at the factory while Odd, Ulrich, and Yumi go back to school. Finally, one more tower is activated and it starts to snow. Then it turns to a blizzard, trapping the three at the school. While they try to get to the factory, the find Sissi, Hervé, and T.V. in T.V.'s car, crashed into a tree. As the tree timbers, Yumi pushes Ulrich out of the way and gets trapped in the process. Ulrich stays with Yumi and Odd goes to the factory. The tower is deactivated before Yumi and Ulrich freeze to death.

Jeremie discovers five activated towers and gathers the group to take care of them. However, when they arrive at the factory, they find a man at the interface, deactivating the towers as if it were a simple matter to do so. When questioned, the man claims that he's none other than Franz Hopper. However, something seems off about this convenient arrival. Franz says that the scanners cause cell degeneration, and blames it and the destruction of his diary on Jeremie. With everyone except Aelita angry at him, Jeremie calls his father and asks to be withdrawn from Kadic in favor of a school for gifted students – but after he hangs up, while pondering his dilemma, he realizes that there is something inherently wrong with Franz's explanation.

When the supercomputer's uranium power source begins to fail, Xana is forced to possess a local criminal named Peter Duncan to replace it. The supercomputer's periodic shutdowns threaten not only Xana, but also Aelita, whose heart stops beating with each shutdown.

When Xana possesses Kiwi, it turns the little dog into the carrier for a virulent virus that turns those it infects into zombies. To make matters worse, Aelita and Jeremie are stuck in the cafeteria and can't get to the factory. On top of that, Odd is a zombie himself. Jermie and Aelita escape but Ulrich and the other students (except William, who is turned into one himself) fight the rest.

While Aelita adjusts to her new life on Earth, Jeremie and the others investigate the mysterious owner of the Hermitage, Franz Hopper, and his link to the supercomputer, Lyoko, and Xana. It is discovered that Franz Hopper was in fact a former teacher at Kadic. After being teased by Sissi, Aelita retreats to Lyoko but gets lost. Jeremie finds her in a previously undiscovered fifth sector of Lyoko, The Carthage Region.

After taking another trip to The Carthage Region and returning to the school, Aelita talks to Jeremie about not being human, unaware that Sissi is recording their conversation. On top of that, the data they had retrieved from the Carthage Region takes over the supercomputer and starts running return trips over and over. Jeremie discovers that returning to the past makes X.A.N.A. much stronger and more powerful. During the third return trip, Xana possesses Sissi with his newly strengthened and increased abilities and powers and goes after Ulrich. Not only does the group have to deal with Sissi, but they also have to stop the return trips from continuing.

After deciphering a part of Franz Hopper's diary, Jeremie gets an idea to make a monster that fights on the side of good. By combining techniques, he makes the Marabounta, a sphere that can replicate itself endlessly and devour any monster it can encase. Though it works quite well to begin with, everything goes wrong when it senses Aelita's virus, which is linked to Xana. After Odd attacks it to save her, the Marabounta goes haywire and threatens to devour all of Lyoko, so XANA sends his monsters to help destroy the Marabounta in order to protect Aelita and her memories. The monsters leave the Lyoko Warriors without causing any trouble.

Ulrich and William get into a fight over Yumi. When Xana activates a tower and materializes Krabbes, he attacks Yumi's house and destroys two scanners. While Ulrich is in detention, Yumi defends her family, and Odd distracts the Krabbe at the factory, Aelita has to make her way to the tower without any support.

Odd decides to start a music band with his friends. But Jeremy can't play, so they try to hire a drummer. In the end, the best drummer they can find is Nicholas (Sissi's blond-haired crony). As the group argues over whether or not to let Nicholas join the band (Ulrich and Yumi: Pro-Nicholas. Odd: Anti-Nicholas, Pro-Naomi), Jeremie alerts them that XANA is planning to overload a pylon and send this massive electric current through the telephone wires to blow up a nuclear power plant. Just in the nick of time, Aelita, Ulrich, and Odd stop XANA's plan. At the end of the episode, Odd gives in and allows Nicholas to be the drummer of his rock band.

Ulrich and Jeremy are doing graffiti on a wall on campus while Kiwi wakes up Jim. When Jim passes Ulrich and Jeremy, Ulrich gets away, but Jeremy just stays there and gets I'm trouble and has to stay in the campus over vacation. Sissy is being suspicious of Jeremy and thinks that he wanted to get in trouble. She asks her father to stay over the campus over her vacation, while she sorta spies on Jeremy. Jim is telling Jeremy to wash off the graffiti, then leaves while Jeremy gives Sissy the sponge and tells her (while mimicking Jim) to wash off the paint and later once again gets in trouble with Jeremy. Meanwhile, Xana has attacked again, this time spilling two toxic chemicals creating hazardous smoke. Sissy claims that she saw the smoke with arms and bumps into Jim who later finds the smoke after not believing in Jeremy and go into a small room where there is no vent and if they try to open the door, they can die. How will Yumi, Aelita, and Odd save the world and how will Ulrick find