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.

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.

Aelita gets mad at Jeremie and she and Odd go into Lyoko without telling anybody, which causes problems. On lyoko, Xana creates a diversion to get everybody to deactivate the tower in The Mountain Sector while the monsters (mostly Mantas and Creepers) worked on destroying the core of Lyoko. Jeremie and Aelita find a strand of DNA that belongs to Franz Hopper, indicating he may be still alive.

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?

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.

The new virtual, submersible "submarine" (as Jeremy calls it) is almost complete, the last step being a secondary program that needs to be run by 4 PM the next day. However, when Aelita and Jeremy stay up late to set the program up, they are caught and given detention. Meanwhile, William takes the opportunity to attack the incomplete ship, forcing Yumi to run the Supercomputer in Jeremy's absence. Odd and Ulrich are unable to handle the situation, but Jeremy and Aelita are able to sneak out in time to help. Aelita is able to repel William with a massive attack, allowing Jeremy to complete the sub on time. It is later christened the Skidbladnir, nicknamed "the Skid" by Odd, after the Norse ship.

When Odd complains that he doesn't have any cool powers on Lyoko like his friends, Jeremie designs him a teleportation power. It works, but ends up leaving duplicates of himself in the location he teleported from in The Mountain Sector. After trying it twice, Jeremie devirtualizes Odd to find out what went wrong, accidentally creating three clones. Meanwhile, in the real world, Xana attacks using a mysterious smoke that turns anyone it hits to stone. One of Odd's copies gets turned to stone, so the other two Odds must retrieve him before they become unstable and disappear.

Jeremie is now taking his ""Materalize Aelita!"" campaign to levels unknown - quite literally. He virtualizes himself, but there isn't enough memory in the system to complete the transfer, and Jeremie is caught between worlds. It will take more memory than the factory has to complete the transfer back to Earth, and if the crew doesn't hurry, Jeremie will be deleted as an old file! Could this be the final frontier for Jeremie? Will Yumi be able to pick up the slack?

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.

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.

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.

During a field trip with the rest of her 10th grade class, Yumi finds herself facing off against the students, teachers, and bus driver, all of whom Xana has possessed. At the same time, Xana plans to get rid of Lyoko through an alternate means: destroying each sector one at a time. To this end, he uses the Scyphozoa to possess Aelita and enter Code:XANA into the way tower, wiping out The Forest Sector, realized by Jeremie.

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.

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.

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.

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.

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?

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, Aelita purposefully wipes out The Ice Sector leaving The Mountain Sector left.

Before leaving Sector 5, Odd and Ulrich are hit by a weird red beam from a pair of Mantas. They both eventually begin to act strange in the real world during a school play. They start seeing their environment, people as enemies, and fight as if they were still on Lyoko. They are branded as insane and hospitalized while Jeremie tries to figure out what happened. After finding the cause and devising a cure, Jeremie has Yumi and Aelita break them out of the hospital. Meanwhile, Xana uses their handicap to mount an attack on Lyoko's core. Yumi heads to protect the core, as Aelita tries to help the boys who instead now see the real world while on Lyoko.

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.

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.

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 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.

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.

Aelita finds a photo of herself with Franz Hopper at the Hermitage, with a mathematical equation in the background. Jeremie discovers that the program works as a reset feature to Lyoko, something not too helpful but useful nonetheless. Meanwhile, Odd, in an attempt to impress a girl in photography class, inadvertently sends the photo to Sissi, who in turn shows it to her father. He questions the group about it, with Jeremie pointing out that Aelita would obviously be twenty-four by now if she were the one in the photo. They are sentenced to dentention in the library by Jim before any more discussion occurs. Before he can follow up on the matter, Jean-Pierre possessed by XANA. He delivers Aelita to Lyoko, where the Scyphozoa is waiting for her. It takes control of her and tries to force her to walk into the digital sea, but Ulrich and Yumi are there to keep her from doing so.

Jim's nephew, Chris, the drummer of the Subdigitals, pays a visit to Kadic to look for an opening act for the band's next concert. Everybody tries out, and Aelita turns out to be the one Chris is looking for. However, circumstances make sure that Chris does not realize who Aelita is, and X.A.N.A.'s clone of him only complicates matters, kidnapping Aelita and sending her to Lyoko. Jim and Chris manage to involve themselves in their search for Aelita, and end up battling the clone while the rest of the group tries to deactivate the tower. After the threat is over, Jeremy executes a return trip so that Jim and Chris remember nothing. He also delivers Aelita's demo CD to Chris personally after doing so.

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.

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.

Having failed to destroy X.A.N.A.'s supercomputer in the Amazon, the group sets out to finish the job. Meanwhile, Odd's bragging gets the better of him, and he makes a bet with Ulrich not to brag for 24 hours. However, circumstances conspire to constantly put him in the spotlight, and when he ultimately both defeats William single-handedly and destroys the supercomputer in the real world, Odd becomes convinced that being a braggart is something he can be proud of.

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.

Both Herb & Jeremy are in a robot competition Herb with ""Iron Sissy"", and Jeremy with ""Kiwi 2."" Herb cheats by launching a gear from Sissy to destroy ""Kiwi 2."" Meanwhile, Xana's latest plan, using the factory to built a robot. Ulrich & Yumi get help from Herb in slow down Xana's robot. Jeremy discover that Xana robot had built in the factory and messed with computer that goes to Lyoko. Jeremy fixes the super computer, and Odd helps out Alieta in Lyoko. After the time reboot, Kiwi 2 dodges Herb's gear to win the contest.

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.

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.

In order to compensate for all of William, while under XANA's control, Jeremie sets to work designing new equipment for his friends and recreating Lyoko. In order to buy himself time to do this, he activates a tower and uses it to create a a clone of his own to attend class in his place. Meanwhile, William's absence is drawing attention, from both the principal and his father. While Jeremie's Clone is impressing Jim outside, William appears on Lyoko and tries to put the tower under XANA's control. In order to maintain his clone, Jeremie draws energy from Sector Five to maintain the activated tower. He eventually runs out of energy and the tower is put under XANA's control. While Odd holds the Jeremie Clone off, Aelita, Yumi, and Ulrich go to Lyoko with new outfits and powers. They eventually deactivate the tower and stop William, who tries to push Yumi into the digital sea. She is saved by Odd at the last second. Jeremie then does a return to the past and replaces the Jeremie Clone with a William Clone to prevent any suspicion about his absence.

Odd tries to take Kiwi to Lyoko, but ends up absorbing him instead. As a result, Odd slowly begins to take on dog traits, such as enhanced smell and scratching himself with his foot. While Jeremy works on separating the two, X.A.N.A. possesses a biker gang to attack Yumi. When Ulrich and Aelita arrive to Lyoko, they are confronted by William and three Tarantulas. Jeremy manages to split Odd and Kiwi while Aelita deactivates the tower.

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?

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.

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 Kiwi's mindless destruction becomes too much for the group to bear, they force Odd to keep him at the factory. As Odd drops him off, XANA possesses Jeremie's Kiwi Two robot, turning it into an army of self-replicating attack dogs. The dogs attack Yumi and Ulrich, among other children, during Jim's Pencak Silat class. After Aelita deactivates the tower and a return trip erases the incident, the group decides that the regular Kiwi isn't that bad, after all.

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.

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.

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 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.

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.

When a director comes to town to film a movie, XANA posseses a plastic alien model in order to destroy Ulrich and the others.

Jeremie learns that he has to take a test. If he passes, he'll get transfered to a new school and nobody will be able to stop XANA. Speaking of which, XANA takes control of a pack of rats. The rats attack the school and makes it nearly impossible to move around. Ulrich, Yumi, and Odd get Jim, Sissi, and everyone else to the roof and then proceed to the lab. Ulrich and Odd are virtualized, while Yumi controls the supercomputer. Does the team stand a chance with Jeremie temporarily gone?

Xana decided to get rid of everyone by using the power of Gravity, and Yumi, Odd, and Jeremy went to the factory, but Ulrich had a soccer game, and his Dad was there, and as Odd said: If you're not first, then you're not good in his book. Ulrich had to save Mrs. Hertz though, because she was in the science lab. So Yumi and Odd went to Lyoko, but a huge swarm of monsters reached them, and Yumi and Odd had to clear a path for Aelita, and Yumi created a rock shield with her Telekenesis, but Yumi's Telekenisis didn't last very long, so Aelita decided to go across another way. She ended up getting hit and she fell off the bridge she was materializing. Odd and Yumi were in disbelief. But, Aelita appeared right behind them. Ulrich slammed through the science lab window, trying to save his dad, leaving Sissy with Mrs. Hertz.

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.

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.

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.

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.

When Odd breaks a mirror, a little bad luck follows and jinxes him everywhere, even on Lyoko. A bug in his virtual avatar spreads to Yumi and Aelita, causing annoying pauses and random devirtualization in the Desert Replika. Meanwhile, at the site of the Replika's supercomputer, X.A.N.A. materializes Kankrelats in the real world to stop Ulrich and Yumi. Despite the bug, their mission to destroy X.A.N.A.'s next Replika ends in success, this time by Ulrich, and Odd's luck returns soon afterwards.

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.

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

When all the student's cell phone goes off in class, it starts Sissy on a petition to save her cell phone--but it's goes awry when Odd breaks into the school's office's locker to get his, Ulrich, & Yumi's cell phone. It turns out that X.A.N.A. is trying to get out board a highly powerful miltiary satellite in space. X.A.N.A.'s target turns out be our heroes.

This episode starts out as Yumi and Aelita are running inside Lyoko looking for the activated tower. Then Yumi suddenly disappears! She comes out of Lyoko exhausted, and looks just fine! Until Yumi Comes into Jeremy's room and takes off Jeremy's glasses and deeply gazes into his eyes and Odd and Urick come in the room and they are shocked. Then Jeremy realizes that Yumi is being controlled by Xana! Then Odd, Ulrich and supposedly Yumi.... get digitized. Yumi breaks out and trys to destroy the factory. Until they find the ""real"" Yumi in an orb and then they destroy the bad Yumi and the show ends.

A new rock song Odd downloads sends him into a coma, and the same song is passed through the school. XANA's new beat is the cause, and he can broadcast it anywhere. The hospital is full to bursting with cases, and Odd's heart gets weaker with every beat it makes. But when the tune starts playing in the factory, will the crew learn that music can do more than just soothe the soul? And, will Aelita be able to save the crew? It's all up to a leap of faith...