The episode starts with Jeremie still trying to materalize Aelita. He calls the team to the factory to show them his latest development: a strand of her hair that he has materalized into a test tube. Unfortunately, he didn't realize that he pressed one button too many, and thus screwed up Aelita's programming by adding in a whole lot of bugs. The result is that, immediately after she successfully enters the code (LYOKO) into a tower, she will be formatted - as in, deleted. And of course, as Jeremie is trying to literally work out the bugs, Xana attacks by putting out shockwaves to shake things up, putting Odd, the two junior journalists, and Kiwi in danger. But is Jeremie willing to allow Aelita to be deleted in order to save his friends?

After seeing laughing gas in Science class, Team Lyoko has to see it again - working for Xana. While working for Sissy in a school production of Romeo and Juliet, Ulrich and Yumi are overcome by the gas, and both Jeremie and Odd get a bit too much at the factory. Of course, this results in a data transfer error, leaving Odd bearly able to walk, much less fight off Xana's hordes of monsters. With Aelita flying solo and three of the team in critical condition, will the crew literally die laughing?

After a quick game of soccer, Yumi heads home for the night, but Odd and Ulrich head in for dinner, and Jeremie is already there. He decides to check on Aelita, and Yumi ends up following him instead. But, while scarfing the desserts the others left behind, he and Ulrich get caught up in a shocking Xana trap. Not only is the lunchroom electrified, the roof may fall in at any time. Even the combined power of the eight kids trapped inside - including Odd, Ulrich, and Sissy - can only delay Xana for a short time. Will Yumi be able to get Aelita to the tower before the room becomes a final resting place for our heroes?

When learning about NanoDoctors, small robots being designed to cure dieases, Ulrich holds some gel that the NanoDoctors would live in. Od pranks him and pushes the gel into Ulrich's face, and some minutes later Ulrich suddenly faints and loses his memory. Strangely, amnesia spreads throughout the school, and Jeremy and Od think it's Xana at work. Yumi and Od are virtualized while Ulrich escapes from Sissy, who's trying to convince him they're in love. Ulrich gets virtualized and re-learns how to fight from Od. They help Aileta deactivate the tower. It ends up being the NanoDoctor's gel habitat was infested by Xana Nano-Virii and got up Ulrich's nose.

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?

Well, it starts off as Yumi wanting to have a party at her house. Of course, Odd jumps into action, and says that he has the Deejay problem all solved, they weren't going to listen to Sissy's music. But, oddly, Jeremy couldn't get a connection with Lyoko. Later, Odd and Ulrich are having sliding contests across the floor, but soon, a picture of the Deejay Odd was getting fell on the floor. Ulrich and Jeremy saw is and they asked who it was. Odd said it wasn't important, and he had some stuff to do. Later, again, Odd saw Samantha, the Deejay he was getting, and obviously, he happened to know her. They got into the Comp. Lab, and Sam wanted to take the most powerful laptop there. Jim went in and saw Odd holding the laptop. He scolded Odd, and he ended up getting out. But, they saw Xana attacking. They went to go and rescue Samantha, as she was still in the lab. Yumi and Jeremy went to the factory. Ulrich and Odd saved Samantha, but when Yumi got to Lyoko, she was materialized as soon as

One day at school, Jeremy notices that Odd, Ulrich, and Yumi are missing. Meanwhile, Odd, Ulrich, and Yumi ARE at school with Jeremy! What's going on? Turns out that XANA (in the form of Jeremy) has trapped Odd, Ulrich, and Yumi in a virtual world identical to the boarding school, completely at his mercy. With Aelita's help, Jeremy reaches the fake school and tries to convince his friends that he is the real Jeremy and that the imposter is XANA. When they learn that Jeremy got into the scanner to come here, XANA claims that Jeremy is the fake because he would never go into the scanner. But the others say that if his friends were in danger, he would. XANA gets angry and tries to crush everyone with wires and holographic zombies of Jim, Nicholas, and Herve. But Aelita destroys the false school just in time, foiling XANA's plan.

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.

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 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.

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 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.

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.

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.

There is a new recreation room at Kadic and William's clone is put in charge of it. Meanwhile, Jeremy has developed a program to get the real William out of Lyoko. However, the program malfunctions and bugs up the tower, allowing X.A.N.A. to take it over while Aelita cannot shut it down. As the William clone lashes out at the group, the real William is on Lyoko to keep the tower under X.A.N.A.'s control. Jeremy manages to repair the tower in time for Aelita to reset it, restoring the clone to working order. With a return trip to the past to erase the unwanted memories of William's behavior at school, the group elects Sissi as the rec room monitor.

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.

Because of a surprise dorm inspection, Odd has to convince Yumi to keep Kiwi at her house. Jeremie, meanwhile, has located the next Replika, a copy of Sector Five. Its supercomputer is located on a newly-built space station orbiting Earth. While Odd and Yumi work to disable it, Aelita and Ulrich work to disable the Replika's defenses of Sector Five, which threaten to destroy the Skid. To make matters worse, the supercomputer is guarded by a trio of floating spheres that can grow spikes and melt through metal. In the end, Odd disables the supercomputer by breaking some cooling pipes in the room and damaging it with water. All the while, Yumi's dad, Takeo, has been having fun with Kiwi, much to Odd and Yumi's surprise.

Odd is presenting one of his films, but is unhappy because his parents are coming. According to him, they never find fault in anything he does, which he finds dissatisfying because he isn't treated like a normal teen. However, when he's finally pressured into it, XANA attacks, using the school's cell phone antenna to spread a virus to everyone who answers their phone to cause them to become vicious, angry mind controlled slaves , starting with Odd's parents. With the widespread use of cell phones, all but the Lyoko warriors and Sissi are affected, Sissi having had her phone accidentally broken by her father. While she and Odd attempt to evade the possessed students and faculty, the others deactivate the tower in the Mountain Sector. Once a return trip wipes everyone's memories, Odd plays his video, which showcases all the humorous moments at Kadic, with Sissi in particular being treated in a positive light as thanks for her earlier assistance, much to her confusion.

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.

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.

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.

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.

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.