With the Skid gone and XANA's Replikas at unmanageable numbers, Jeremie continues work on his multi-agent system. Meanwhile, Aelita has nightmares about her father being killed by XANA. As Jeremie works, he is contacted by Franz Hopper, who arranges a meeting on Lyoko. William wants to help, but all except Aelita are a little wary of trusting him again. William is left in the lab with Jeremie. After meeting up, Franz transmits the data necessary to finish Jeremie's multi-agent system. However, XANA is not willing to give up without a fight, activating a tower to possess William once again while sending the Kolossus to deal with Franz. Yumi willingly devirtualizes herself and fights William while the others protect Franz. Once Franz is finished transmitting the data, Aelita and Odd head to Sector Five to finish the program. Ulrich, meanwhile, manages to defeat the Kolossus, but its corpse falls on Ulrich, devirtualizing him instantly. However, a problem arises: the energy requirements are too great. Aelita's nightmare is realized when Franz makes the ultimate sacrifice himself to power the program, and in doing so XANA is wiped out completely. Though a great victory for them, the loss of Franz Hopper leaves them with little reason to celebrate.

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.

After William is initiated into the group, a series of events leaves only him and Aelita to defend Lyoko's core. During William's first mission to Lyoko, Xana uses the Scyphozoa to possess him, making him the general of a massive army focused on Lyoko's core. Despite their best efforts, the group can't stop the possessed William from destroying the core, which both renders the supercomputer useless and transforms William into a darker, Xana-themed version of himself. Later, in the Hermitage, while the group broods over their predicament, Jeremie receives a coded message directly from the internet, sent by none other than Franz Hopper who somehow survived the destruction of Lyoko.

As Jeremy is perfecting his materialization program for Aelita, Yumi, Ulrich and Odd are making preparations for her arrival. But as success comes within their grasps, Jim's paranoia aggrivates the already bad situation started by XANA. Due to his injured ankle Jeremy has no choice but to reveal the existance of Lyoko to Jim so he can get to the warehouse. In the end XANA's attack is stopped and Aelita has finally been materialized into the real world. Or has she?

Aelita is materialized, but unfortunately, Xana implanted a virus inside of Aelita, so if Xana dies, so does Aelita. Then Xana decides to attack with bringing his own monsters to Earth. Ulrich and Yumi fight off the monsters, while Odd goes to Lyoko with Aelita. Odd eventually get materialized himself, but luckily, Ulrich and Yumi reach the factory, and fight off the last Hornet, attacking Aelita. She deactivates the Tower, and on the second run, the gang is talking with Aelita, about finding an anti-virus, but Aelita can still be materialized for small visits. So they look ahead to the future, and the episode ends.

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.

With their mission completed, the group looks back on all their fond memories of Lyoko. Sissi, meanwhile, plants a tracking device on Ulrich in order to discover their secret. When it comes time to shut down the supercomputer, all but Yumi are unwilling to go through with it: Aelita is still holding onto the hope that her father can somehow be saved, Jeremie doesn't want to take away the thing which made them friends, and Odd and Ulrich both liked being heroes. While they muse over their attachments to Lyoko, Sissi finds her way into the computer lab, and Jeremie's open diary reveals the whole of their adventures. When Sissi tries to explain this to her father, he believes she has lost it and sends her to the infirmary. A return to the past deals with that problem. Ulrich stops Sissi from planting the tracker on the repeat attempt, and the quintet invites her as a friend. Once more at the supercomputer, the group unanimously decides to shut it down, closing the book on their adventures, for now.

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.

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.

Using the data that Franz Hopper gave them, Jeremie and Aelita succeed in recreating Lyoko, which now holds only Sector Five. Soon after, William is devirtualized, and seems perfectly normal. Sissi decides to make herself "editor-in-chief" of Kadic News, much to Milly and Tamiya's dismay. She soon barges into Aelita's room to interview her and is stopped by William. As soon as William makes Sissi, timay and milly leave,William kidnaps Aelita and takes her to Lyoko. William leads Aelita out of Sector Five and to what used to be The Desert Sector. His intent is revealed to throw Aelita into the Digital Sea. Odd manages to stop him, but William dives into the digital sea. Jeremie concludes that this is Xana's new strategy, and that they must be careful.

When an embarrassing picture of Yumi is printed in the Kadic newspaper, she turns to Odd as the source. He manages to get Ulrich to take the blame, however, causing tension between him and Yumi. Putting that aside, Jeremie sets up a mission to the next Replika, a copy of the Ice Sector. Its supercomputer is located in Siberia, where XANA is growing brains for an unknown purpose. Odd and Yumi are sent to the real world to destroy it, only to be confronted by William. When trying to shut down the tower, Aelita realizes that the data it is generating could be used to free William. After downloading the necessary data and disabling William, everything seems to be set for destroying the Replika. However, XANA draws on the power of his many Replikas to create a new monster: the "Kolossus," a massive creature resembling a fire elemental with a sword for a hand. It easily devirtualizes Aelita and Ulrich, and nearly destroys the Skid, as well. With this new development, and the realization that XANA has hundreds of supercomputers at his command, Jeremie has to change strategies. Meanwhile, Yumi forgives Ulrich for the picture, and Odd admits to his deception soon after. Yumi gets back at both of them by getting a picture of the two coming out of the shower in the paper.

Ulrich is getting tired of getting being rebooted so many times and waiting to find out if Yumi has feelings for him or not. He thinks these are his only troubles, but he is not counting on two things: 1) Sissy getting in the way again and 2) Xana's latest attack which is quite deadly. He disconnects the scanners that makes the return to the real world if he or any of the gang lose all their life points. Instead of returning devirtualized, they could die in Lyoko. Can Aelita shut down the tower in time?

It's holiday time at Kadic and everyone is headed home. Aelita, however, has no home to go to. As she watches over Lyoko, she gets a message from Franz Hopper, who has constructed a simulation bubble of their mountain home on Lyoko. Though happy to see her father, Aelita quickly learns that the entire thing is a trick from X.A.N.A. – her father is just an illusion in the simulation bubble on Lyoko. William is there waiting for her in order to throw her in the Digital Sea. However, she escapes resulting in William chasing after her. The rest of the group, having been unable to contact Aelita, follows her onto Lyoko, but they fail to keep William from throwing her into the Digital Sea. When it seems as though Aelita is gone for good, she is lifted from the sea by the real Franz Hopper, who has manifested himself as a floating white bubble with a pink aura. After dropping her back on Lyoko, he returns to the Digital Sea.

In order to defeat XANA, whom they have vastly underestimated, Jeremie plans to design another multi-agent system to combat him. That, however, is still under development. In more immediate matters, Jeremie has figured out how to free William from XANA, but needs to run his program directly from the Ice Replika supercomputer. Meanwhile, William's parents arrive to visit their son, and the strange behavior of his clone concerns them greatly. Back at the Replika, William and two Mantas come to try to sever the translation. However, the Mantas are quickly destroyed by Yumi and Ulrich. William then jumps into the digital void and comes back up with the Kolossus. Jeremie uses some new tricks to stop the Kolossus, allowing Aelita and Odd to reach the supercomputer without worry. However, an army of robotic drones now stationed at the facility complicates matters and they de-translated Odd. With much effort, Aelita is able to run the program to free William before she is de-translated also, but their victory comes at a cost: though William is saved, the Skid is destroyed by the Kolossus with Aelita in it. Fournately, she is devirtualized before the Skidbladnir was totally destroyed. Back on Earth, William is able to take his clone's place, pacifying his concerned parents. Ulrich, meanwhile, has to deal with William's affection for Yumi once more.

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.

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.

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, Susan, disappointed with Ulrich's bad grades, tries to place him in remedial classes.

The group turns to Jim for training, so they can be better prepared to fight against X.A.N.A.. However, things go bad when X.A.N.A. possesses a boar to attack them with, forcing them to put their training to good use to avoid it. Furthermore, X.A.N.A. sends William and a group of Mantas to attack Lyoko's core. Jeremy stays behind to help Jim while the others repel the attack. Jeremy risks his life to save Jim when the two encounter their attacker in a cave, and Aelita deactivates the tower in time to save them both.

Hiroki steals Yumi's diary and Ulrich finds it. Meanwhile, in a new attempt to free William from X.A.N.A.'s evil clutches, Jeremy creates a program to find William in the Digital Sea. When he uploads the program to the Skid, the sonar becomes bugged, forcing the gang to return to Lyoko. When the Kongers interrupt their return, Yumi gets stranded, and is lost in the Digital Sea. X.A.N.A.'s attempt to take advantage of this alerts Jeremy, allowing him to direct his friends to Yumi. After fighting off the Kongers and William, who has his own ship (the Rorkal) to travel in, they return to Earth. To help Hiroki apologize to his older sister, Ulrich secretly returns the diary.

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 being rejected by Yumi, William makes it his mission to find out the secret she's hiding. Soon enough, he manages to follow Ulrich and Odd to the factory and learns about Lyoko and Xana. Meanwhile in The Ice Sector, the Scyphozoa possesses Aelita to enter Code:Xana in the way tower, but is devirtualized just in time. The group thinks William's help is going to be quite useful, when a possessed demolition worker sets several bombs in the factory. They take a vote as to whether or not to include William as part of their group, but Yumi votes no and Jeremie initiates a return to the past.

Jeremy, Aelita, Ulrich, and Odd go with the rest of their science class on a field trip to an island in the middle of a nearby lake to study water-based plant life. Yumi, not part of the class, remains behind to sit through two important exams. Jeremy's fears about X.A.N.A. attacking at such an inopportune moment are realized when X.A.N.A. creates an electricity-blasting sludge that attacks anyone who approaches the shore. Yumi is forced to go to Lyoko alone. She fights William and during their fight is able to reach his true mind and personality. Though X.A.N.A. soon manages to regain control of William, Yumi is saved by Aelita, who escaped the island on Sissi's bike. Aelita is able to deactivate the tower and Yumi claims that one day they will bring William home. She initiates a return trip to the past and the class is saved from electrocution.