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.

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.

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.

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.

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.

The gang manages to convince Jeremy to let them test out the Skid. During this test, the navigation system bugs up, leaving the gang stranded in the digital sea. Jeremy runs to his room to fetch the backup programs, but forgets that it's Fire Safety Day and runs into several teachers, eventually having to scale the roof to get to his room. Meanwhile, the Skid stumbles upon another Lyoko and is attacked by two eel-like monsters. Jeremy is able to repair the navigation system and bring his friends home, after which he surmises that the replica of Lyoko is created from the portion of the Keys to Lyoko that X.A.N.A. has stolen from Aelita's subconscious in the second season finale, The Key. Jeremy wonders how he plans to use it.

Jeremy decides to teach Odd, Ulrich, and Yumi how to use the Supercomputer in case he or Aelita are unable to, being X.A.N.A.'s favorite targets. During the lesson, Jeremy is attacked by one of X.A.N.A.'s polymorphic clones, leaving the others to operate the Supercomputer without help. Aelita is at the final audition with the Subdigitals, competing against two other candidates, and thus cannot be contacted. To make matters worse, the clone heads for her after dealing with Jeremy. Using what they learned from Jeremy, the others are able to rescue Aelita and deactivate the tower without his help. Aelita is also chosen as the winner of the audition despite her walking out on them.

The group travels to one of X.A.N.A.'s replica sectors in the Digital Sea. Meanwhile, Aelita and Odd get into a fight after Odd's desire to sleep in gets them both in trouble. Furthermore, their arguing inadvertently leads Nicolas and Herve into the factory, where Jeremy is forced to distract them while the group explores the Lyoko copy, which consists entirely of the Forest Sector. On the Lyoko replica, William and a pair of Megatanks arrive to destroy the Skid, the destruction of which would cut the group off from the Supercomputer. Odd and Aelita refuse to work together when they first arrive, but eventually resolve their differences and take William down. Jeremy surmises that another supercomputer is controlling the Replika (what the Lyoko copies were dubbed as), and in order to get rid of it, he'll have to find a way to materialize his friends at the location of the supercomputer.

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 a comet passes near Earth, X.A.N.A. uses a laser-equipped military satellite to split it into chunks, simultaneously aiming the bulk of it directly at the factory. Aelita, Odd, and Ulrich are exploring the digital sea at the time, and X.A.N.A. traps them with a firewall to prevent them from stopping the attack. Meanwhile, Yumi is stuck at school and, when informed of the attack, works to evacuate the school. Jeremy tells Yumi to connect his laptop to an antenna to tap into the military satellite and destroy the comet. She does so with help from Hiroki and Johnny. However, X.A.N.A. prevents them from doing so. Unable to stop the attack, Aelita reasons that X.A.N.A. is more concerned with taking her prisoner than destroying the Supercomputer, and to test her theory, she has Odd devirtualize her. Having guessed correctly, she watches as X.A.N.A. destroys the comet and calls off his own attack on his own accord.

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.

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.

Jeremie has perfected his "Teleportation" process, allowing him to send his friends to the location of Xana's supercomputer in the real world to destroy it. He uses it on Aelita and Odd first, sending them to the jungle laboratory containing the supercomputer. As they explore, they find that XANA is constructing cybernetic spiders with the help of a team of possessed scientists. Before they can stop him, however, William manages to sever their connection to the real world, bringing them back to Lyoko in the middle of their mission. In a side story, Yumi is angry with Ulrich because he has forgot her birthday, so Odd promises to get Yumi a present for him because Ulrich has detention.

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.

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.

Jeremy has developed a program to make the William clone smarter, but the learning curve is still problematic, as it tries to fling a glass into the air from a fork. Milly and Tamiya, overhearing the group's conversation about the clone, decide to ask him personally. The clone, having never been told to keep the information a secret, reveals everything to them, and even takes them to the factory. Meanwhile, Jeremy plans a mission to the next Replika, a copy of the Desert Sector. During the trip, William emerges from a scanner and tries to destroy the supercomputer. With the help of Milly, Tamiya, and the William clone, he is defeated, and a return trip keeps Milly and Tamiya in the dark about the Supercomputer.

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.

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.

Jeremy wins a contest to take a flight in an armed fighter jet, even though it is Odd who entered him into the contest. However, just before takeoff, X.A.N.A. possesses the jet and sends it to destroy the factory and kill Jeremy by forcing it to crash. As it closes in, Aelita, Odd, Ulrich, and Yumi struggle against William, who devirtualizes them one by one in his attempt to throw Aelita into the Digital Sea. Ulrich is the one to come out on top in a blade to blade fight with William, and Aelita is able to deactivate the tower. A return to the past is launched before the factory is destroyed, and Odd gets his chance to ride in the jet afterwards.

When Sissi's pen pal from Iceland, Brynja Heringsdötir, arrives at the school, all the boys swoon over her, making Sissi envious. When Brynja takes an interest in Odd, he ends up showing her the Supercomputer. While there, she messes with the computer despite Odd's pleas not to, creating a glitch in a program Jeremy is installing that causes every virtualization to happen in the wrong sector and prevents materialization. This becomes all the more problematic when William catches Aelita alone on Lyoko. When forced to choose between his friends and his new love interest, Odd initially stays with her, but decides that his friends are more important. After rescuing Aelita from William, they make up. As Brynja has not been told anything about the purpose of the Supercomputer, nor does it appear that she even cared in the first place, they have no need to perform a return trip to the past before she leaves.

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.

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.

Jeremie's cousin, Patrick, comes to visit. Jeremie isn't entirely happy about it, since Patrick is "super cool" compared to him. Discovering another Replika, Jeremie and his friends plan a mission to destroy it, leaving Sissi alone with Patrick. She is able to convince him to let Herve rummage through Jeremie's computer files. Herve discovers Aelita's forged documents and the program running the Skid, his efforts to decipher it inadvertently draining the Skid's power. To make matters worse, XANA possesses both him and Sissi to cause even more damage. Jeremie, meanwhile, deduces that it's his computer back at school causing the damage, and works with Patrick to stop them. Once the attack has passed, Jeremie has Aelita run a return trip to undo the damage caused. The second time around, Jeremie is a bit more appreciative of his cousin, since the two worked well together before. But, unfortunately Patrick goes back to his own school.

Aelita's first concert with the Subdigitals is coming up, but Aelita's stage fright threatens to get the better of her. Odd meanwhile, has to find an extra ticket so he can bring a date. When the concert finally starts, XANA attacks, possessing Sophia, in order to kidnap Aelita. He also possesses Milly and Tamiya for some extra help. While Ulrich battles the two reporters, the others work to shut down the tower, all while the Subdigitals' music plays in the background. Once the threat is over, Jeremie activates a return to the past so Aelita won't miss the concert.

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.