In a side story Ulrich tries to tell Yumi how he has always really felt about her. However Yumi's platonic friendship with William plays on his doubts.

XANA now wants to take back its power - source codes that were implanted in the electromagnetic parts of the bodies of Aelita, Odd, Ulrich, and Yumi during the time of its supposed "destruction" in order to gain control over the world network once again. The endless virtual war against XANA is far from over, and the five Lyoko Warriors are back in action.

Meanwhile, Jeremie informs his four friends that he has programmed a new vehicle that is made for travelling through the Cortex easily called the Megapod. Once on the Cortex, they are impressed by the new cruiser, which Yumi ends up driving. Unfortunately, Laura follows William to the factory and discovers the lab and Supercomputer, which she is very interested in. During a battle with several Krabes, Aelita, Odd and Ulrich are devirtualized, leaving Yumi trapped in the Megapod. With Laura's help, Jeremie fixes the bugged vehicle and Yumi is returned to Earth just before the Megapod falls into the Digital Sea.

Back in the lab, the team debate about whether they should accept Laura into their group. Aelita, however, is still resentful and distrustful of Laura and launches a return to the past so that she will not remember anything.

Soon after deactivating the tower, another one appears. Odd, Aelita and Yumi cannot return to Lyoko as they were there not long ago, so it's up to Ulrich and William to put their differences aside and get Ulrich to the tower to deactivate it. At first the two are showing off and trying to outdo each other, but after William saves Ulrich from falling into the Digital Sea, they call a truce, allowing Ulrich to deactivate the tower. Once back on Earth, William is fully accepted into the group as the sixth Lyoko warrior.

In Sector Five, Aelita goes to the spot where she last saw her father, and asks if he has anything do with XANA being reborn and resurrected. Jeremie suddenly alerts a saddened Aelita that a tower is activated in the Desert Region, and goes to deactivate it before Yumi, Ulrich, Odd and William engage in battle with the three duplicates of the boy. Surprisingly instead of attacking XANA fixes the sound system that broke and leaves without any trouble.

Meanwhile, Jeremie's computer is set on repairing a corrupted video file recovered from the Cortex. Eventually the task is completed and the gang watch the clip of Franz Hopper, furious at an employee who stole some documents of his. He fires the man and storms out, but the man remains in the room and laughs, calling Franz too naïve. Aelita identifies the man as Professor Tyron though she had never heard of him before.

Meanwhile, Ulrich and Yumi encounter Ninjas in the Cortex for the first time, but are unable to defeat the new monsters and are sent back to Earth in no time. Laura agrees to keep the factory a secret and to help them out with programming to destroy XANA once and for all when they need her. With little choice, they welcome her into the group as the seventh member of Team Lyoko, which she gladly accepts.

A specter with hypnotic abilities appears the same day. If the specter manages to catch someone's gaze, it can send them into a trance-like state which the specter can use to approach a Lyoko Warrior and take their actual source codes without them fighting back. Ulrich manages to test the false source codes and destroys the specter, but it knocks him unconscious for a while. Jeremie decides not to try it again as it is too risky.

With the advice given by Ulrich, and a new-and-improved, unusually effective bo staff weapon programmed for Yumi, in addition to her Tessen fans, she manages to defeat the three Ninjas easily and gathers the data. In it they find a video clip of Professor Tyron addressing several humans dressed in ninja-like costumes.

Ulrich wins the competition and gives his trophy to Jim, thanking him greatly for his advice.

Aelita then goes to the meeting place and finds a blonde-haired woman there; her long-lost mother, Anthea. They share a warm mother-daughter embrace. Jeremie offers Laura the controls and goes to find Aelita, realizing her "mother" is actually a spectre, and tries to convince her of it. Aelita doesn't believe him and returns to the spectre.

Meanwhile, Laura figures out XANA's strategy: activating the two towers one after the other in a specific sequence of prime numbers. She relays the information to Odd and Yumi on Lyoko, who then enter the towers at the right moment and deactivates them, destroying the spectre in Aelita's arms. Aelita feels remorseful her actions, but the gang all stick up for her, firmly assuring her that she is not alone. As Laura leaves, Aelita thanks her for her help.

Meanwhile, the others explore Lyoko looking for the activated tower that's nowhere to be found. Jeremie eventually picks it up in the Cortex and sends them there to take care of it. When Laura and her dad arrive, Aelita goes back to the lab to get them out of Jeremie's way so the mission can be completed. The tower is deactivated and a return to the past is launched. The group decides to keep Laura in the group, but to only include her when she's absolutely needed and intend to keep her under strict surveillance from now on.

Jeremie then notices that XANA had used the tower as a diversion to attack the Skid with a virus while they weren't looking. Odd is the only one who can go in and must pilot the bugged-up Skid and try to counter the virus with little experience doing either. Laura is called in to help, but they don't make much progress. Jeremie then decides to send Laura into the Skid to help on site, and she becomes extremely excited about the idea. Aelita, however, quickly guides Odd through the steps and together they counter the virus just before Laura is about to be transferred. The Skid is returned to normal and Laura leaves, furious about not having to go to Lyoko after all.

The gang make it up to Odd for his amazing solo work by setting him up with Samantha with the thousand roses he purchased. She is touched by Odd's gifts, and warmly kisses him on the cheek.

Meanwhile, a Ninja, not defeated in the fight in the Cortex, follows the Megapod back to the Skid, then hangs onto the Skid all the way back to the hangar in Sector Five. William ends up being left alone to fend off the Ninja, which is heading for the Core of Lyoko itself. Ulrich is called in and easily destroys the Ninja with his sabers, but it plants a sinister-looking device on the bottom of a platform in Sector Five before it disappears.

Odd then formulates a protection plan where the "codeless" protect the people who can't return to Lyoko for 12 hours, and who have nowhere to hide from XANA's spectres. Another tower is activated and Ulrich and Aelita are shut in a closet under Odd's protection while William and Yumi are sent to Lyoko. William seems upset about being referred to as "codeless," as it means he can't deactivate towers, and isn't considered as important as the others. When he and Yumi reach the tower they're confronted by an evil clone of William who plays on his doubts, telling him that he's being used by the gang, especially Yumi. He and the clone then chase after Yumi while the footballer spectre finds Ulrich and Aelita and corners them.

Odd realizes that the sound system can be used to disrupt the spectre and stop it from advancing, so he starts singing Frère Jacques over the PA to delay it, angering Jim. Meanwhile, William turns on his clone, allowing Yumi to get to the tower and deactivate it.

The gang decides they'll have more luck finding out why by going to the Cortex, where XANA currently lives. They happen upon a huge battle between Tyron's Ninjas and XANA's monsters in the Dome, and can't figure out why the two are fighting each other because Tyron's Supercomputer is what's allowing XANA access to the network. Jeremie decides to organize a meeting with Tyron himself to ask some questions. Later that night the gang goes back to the factory, Aelita and Yumi being sent in to talk to Tyron about XANA. Tyron claims he knows nothing about the artificial intelligence, and that there was no way it could be living inside his own supercomputer. He then has two of his ninjas try to imprison Aelita and Yumi inside the Cortex, but Jeremie pulls them out just in time. It's then that the six Lyoko Warriors realize they are up against two separate, dangerous threats rather than just one.

Aelita sends the others to Sector Five to search for any kind of tracking device that the Ninja from episode 14, Intrusion, could have planted while it was on Lyoko. They find it but don't manage to destroy it, as when it's damaged it sends out an electromagnetic pulse that causes the Lyoko Warriors pain. They decide to dispose of it in the Cortex, carefully removing it from the bottom of the platform and taking it to the Replika in the Skid. XANA retaliates in the Digital Sea by sending Kongres, but they manage to make it there.

Meanwhile, Laura accidentally lets Graven know about her knowledge of quantum physics, and he surmises that she must have something to do with Lyoko, showing her holographic images of Aelita, Odd, Yumi, Ulrich and William's virtual avatars, asking her if she recognizes them. She denies it, but Aelita comes in and tells her that Tyron found the Supercomputer, and that she must come immediately. Graven forces the girls to take him to the lab. Ulrich disposes of the tracking device and everyone comes back to Earth just as Graven enters the lab with the girls. Jeremie launches a return to the past. At the beginning of the day again, Graven gets a phone call saying they lost Lyoko's signal, and to abort his mission. He leaves as the gang watches on. Laura pulls the scientific institution's card out of her bag, studying it, still very interested in the idea.

By the time they reach the center of the Cortex, only Aelita remains. She accesses the mainframe and finds a webcam stream of Tyron working in his lab at that very moment. She observes the stream for a minute, telling Jeremie what's going on, then moves to infect the Cortex with the virus. But then she looks up, and sees her mother, Anthea Hopper, in the office with Tyron, also working on part of the project. After a moment of confusion, Aelita firmly insists on destroying the Cortex and XANA along with it, but Jeremie and the others unanimously decide to abort the mission for now as there is proof that Aelita's mother is indeed alive and a chance of reuniting her with her daughter. Aelita comes back to Earth, upset about not destroying XANA, but her friends convince her that the risk was worth it. Jeremie assures her that if XANA gains 95% of its strength, they will destroy it and the Cortex immediately; no questions asked.

Jeremie can't bring the others back or even send William to help because of the damage to the scanners. The specter then tries to throw Yumi into the Digital Sea. Odd enters the Desert Way Tower and Jeremie uploads the codes they stole from the spectre into him. Odd races to the activated tower with the spectre in hot pursuit. He enters the tower and reaches the floating panel, but the spectre then enters the tower after him. Odd deactivates the tower moments before the spectre touches him.

Meanwhile Aelita resorts to social networking to try to find her mother. After the mission Jeremie tells her the good news: they were able to steal 4% of XANA's power and Odd is capable of deactivating towers again. Aelita then tells Jeremie the good news: she is getting dozens of responses about her long-lost mother as dozens of people all over the world join the effort to find Anthea.

In the end, Aelita is able to speak to her mother, convincing her that she is alive before she, too, is devirtualized by Ninjas. The experience initially leaves her feeling sad, but after Jeremie assures her that Anthea did get her message, her spirits are rekindled.

She sends him into the Cortex, but when he arrives, he is greeted by a massive army of Krabes and no Megapod. Not soon after, the Scyphozoa makes its reappearance, ready to possess William as XANA's servant once again. It captures William and it's up to Yumi, Aelita, and Ulrich to set him free again. A furious Jeremie permanently excludes Laura from the group and launches a new modified version of the return to the past to have her memory fully erased for defying him and the rest.

Ulrich and Odd go into the Digital Sea to track down the hub that sent the packet. But when they start collecting the data, a huge tentacle emerges from the hub and ensnares the Skid. Malware is sent to the Supercomputer, shutting the holomap and superscan down. It was all a trap laid by XANA, and Jeremie can do nothing against it, nor can he devirtualize Odd and Ulrich as the Skid's protection shields slowly fail. Aelita is called in and comes to the rescue, bringing the boys in just before the Skid shatters. Jeremie loses all hope and begins to doubt his own abilities. Yumi goes to Lyoko to search for activated towers while Aelita and Jeremie work on fixing everything. After accidentally endangering Yumi's life, a depressed Jeremie leaves. Aelita saves her and then comes back to the lab to find Jeremie gone, but she cannot go after him because a tower is activated. William is sent in to help, but against an army of duplicating Kankrelats they go nowhere. A specter of Ms Hertz attacks Aelita in the lab, and when Jeremie hears about it he runs back to the lab to help, fixing the holomap and figuring everything out so that the tower can be deactivated in time before Aelita is drained of any more source codes.

Meanwhile, Laura finds the card that was given to her in An Assured Professional Future. Not remembering where she got it from, she dials the number, arranging for a meeting via a webcam video. Tyron speaks to her in person, but becomes disinterested in her when she reveals that she has never worked with a quantum supercomputer before. Just before hanging up, Tyron shows her the holographic images of Odd, Ulrich, Aelita, Yumi and William's virtual avatars, asking them who they are. Laura tells him that they look just like Jeremie Belpois' best friends. Tyron hangs up and thanks her greatly for her help, leaving Laura upset and offended.

On Earth, XANA has stolen Ulrich's codes as well. Realizing that Yumi is on Earth too, XANA sends the specter to find and recover the codes. After locating Ulrich and coordinating with Odd, Odd is sent to provide William and Aelita with backup while Ulrich locates and escorts Yumi to the factory. After arguing with Jeremie over Yumi's safety, William devirtualizes himself in order to find her. Odd goes to Lyoko while Aelita is being pursued by Kongres in the Digital Sea. After Ulrich calls Yumi to find where she is, she's spotted by the specter. William and Ulrich team up to go look for Yumi, but split up after finding her phone, but not her. While in Lyoko, Odd is pinned down and out of ammunition, the Bloks are pushing him towards the Digital Sea. Aelita shows up in the Skid and destroys all the monsters.

Yumi is attacked by the specter, but rescued by Ulrich. After deactivating the tower, it is revealed that XANA has regained 95% of its power. Keeping the promise, it is decided that the virus that Jeremie, Laura, and Aelita have been working on will now be used for destroying Tyron's supercomputer, and preventing any further communication with Anthea Hopper.

Tyron suddenly has a dilemma on his hands: If he turns his supercomputer on and recreates the Cortex, the virus will activate and destroy his system in full. Despite this, the Lyoko Warriors have only won part of the battle. XANA and Tyron are both rendered neutralized but not destroyed. Also, Tyron has all the time he needs to find a way to counteract the virus. There's also the problem of his guardianship to deal with, as well as Aelita and Anthea being finally reunited. As ever, the six Lyoko Warriors must remain on their guard as they begin a new mission; the one to keep their family together at all costs.