After discovering Aelita's link to the supercomputer and the inability to shut off the supercomputer that stems from it, Jeremie works hard to find new and better ways to fight Xana. To that end, he develops new vehicles for the group. He also develops a new tower-scanning program that instantly detects activated towers, allowing Aelita to live on Earth. While adjusting to her new life, the class takes a trip to the nearby woods for a scientific field trip. Ulrich wants to partner up with Yumi, but she's already partnered up with someone named William.

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 discovering The Carthage Region, the group decides to explore it. Yumi is forced to opt out after her continued late-night trips to Lyoko draw the attention of her parents. While on The Carthage Region, Ulrich and Odd get dematerialized but don't appear in the real world, so Yumi sneaks out of the house to go to Lyoko and rescue Aelita from the Scyphozoa while Jeremie searches for a way to recover Odd and Ulrich. Unfortunately, Yumi's parents discover that she is missing and alert the school, who in turn discover that the other four are missing as well.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

It's nearing the end of the year and Jeremie's research has hit a dead end. After the group collects some data from The Carthage Region, he plans to use a tower to decipher Franz Hopper's diary. Before the mission, Odd gets a message from a mystery girl. When he goes to meet her, he is attacked by one of Xana's ghosts and locked inside a well at the Hermitage. The ghost then assumes Odd's form and goes to Lyoko in his place. The tower that Xana activated to make the ghost then deactivates, confusing Jeremie. Putting it out of his mind, he begins his plan to decipher the diary. Shortly after they begin, the ghost turns on the group, devirtualizing Yumi and chasing Ulrich away from the tower as three Tarantulas arrive to protect it. At the same time, Xana attempts to take over Jeremie's tower, locking the decoding procedure so they can't abandon it. Jeremie realizes the true nature of the ghost during the fight, and Yumi goes off to find the real Odd. After the ghost proves to be ineffective against Ulrich, it shape-shifts into a clone of Ulrich. In this form, it proves to be an equal match for him. After much fighting, Ulrich finally beats the clone, but is taken out by a Tarantula shortly after. Just when it looks like Jeremie's tower will fall, Franz Hopper steps in and protects it. The diary then decodes fully. After examining the diary, Jeremie tells Aelita that she is Franz Hopper's daughter.

After going through all of Franz Hopper's diary, Jeremie discovers the truth behind the supercomputer, at least to some extent. Hopper had used it quite extensively, to the point of repeating a single day for more than seven years. His sanity degraded throughout the experience. Hopper also revealed that he and Aelita hold the keys to Lyoko, which Xana was after. He only needed her half, now. The keys would allow him to escape the supercomputer. Jeremie also finds a way to free Aelita from the supercomputer. It turns out that Aelita never had a virus. In fact, Xana had been holding onto a piece of her, which was responsible for linking her to the supercomputer. Aelita is not willing to go, angry over the fact that Hopper had essentially taken her life from her. She's also worried that Xana might escape. To that end, she shuts down the supercomputer. Jeremie rescues her, and the group goes to Lyoko to retrieve her fragment. After all their efforts, they seem to succeed, but it turns out to be a fake. Xana manages to devirtualize Aelita's defenders and steal her memory, effectively killing her and allowing him to escape, which shuts down Lyoko in the process. His escape allows Franz Hopper to revive Aelita and Lyoko, restoring all of Aelita's memories in the process. Through the restoration, Aelita finally remembers her past up to the point that she went to Lyoko. With Xana now free and Aelita's memories returned, neither are linked to the supercomputer. This means that they could shut it down, but it would do no good. Unsure of how they'll proceed, Jeremie promises that they'll find a way to stop Xana.