Code Lyoko: Evolution is the sequel to the French animated television series Code Lyoko. Set one year after the events of the original series, Jeremy Belpois, Odd Della Robbia, Ulrich Stern, William Dunbar, Yumi Ishiyama and Aelita Schaeffer return to their daily lives and routines at Kadic Academy. XANA, despite their success in defeating it previously, suddenly reappears, reborn with even more strength and power than ever before. The protagonists resume their former double lives in order to protect humanity from XANA's evil schemes once again. Joined by William Dunbar, who has finally been accepted as the sixth Lyoko warrior, and an unreliable girl-genius named Laura Gauthier, the seven heroes are bent on unraveling the reasons for such a return and to exterminate the malevolently evil sentient, autonomous artificial intelligence/multi-agent system that is threatening the world once again.
Jeremy and Aelita program false source codes that will destroy any specter that tries to take them from a Lyoko Warrior, and tests it using Ulrich as a guinea pig. Ulrich is told to wait at school until he spots a specter and deliberately touch it to transfer the fake source codes to it to test if they work. 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. Jeremy decides not to try it again as it is too risky.
Jeremy tries to create a virus to destroy the Cortex, however it doesn't work and the group discusses what to do. They decide to bring Laura to the factory and Odd steals her tablet and runs, with Laura chasing after him. When she gets there the gang explains about XANA and the Cortex and that they need her help, which she accepts to give. She easily fixes the problem and they launch the virus and a return to the past. Laura forgets everything, but thanks to a few hidden commands in the virus, the code for the return to the past was altered to exclude Laura, causing Laura to start having memory flashbacks of her time in the lab. She follows the memories to the sewers. William (who was left on Earth) tries to stall her, but fails, and Laura ends up back at the lab. 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.
After successfully reprogramming the Skid, Jeremy and the four other Lyoko Warriors discover another Replika in the Digital Sea called the Cortex. They intend to learn more about this mysterious, ever-changing sector. Meanwhile, William finds himself accepted temporarily into the group and aids them in the Cortex. Aelita also finds something very mysterious about her late father in the Cortex's interface.
Samantha Suarez - Odd's former sweetheart and girlfriend - enrolls at Kadic, and the boy eagerly pursues her. At the same time, he is being pursued by a polymorphic specter, which XANA is able to create due to its new increase in strength and power. The others go to Lyoko to deactivate the tower but are all devirtualized by a giant wall of Bloks. Odd destroys the wall using a scanner eyepiece programmed by Jeremy and deactivates the tower. Meanwhile, Jeremy'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.
The gang return to the Cortex to get data on the mysterious Ninjas. Ulrich opts out of the mission because he has a karate competition to attend, and Jim won't let him skip it. The others don't fare well against the Ninjas until Ulrich arrives, offering them advice that Jim passed on to him; be unexpected. With the advice given by Ulrich, and a new-and-improved, unusually effective bo staff weapon programmed for Yumi, 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.
A computer error causes the science test scores at Kadic to be messed up, as well as bugging up the rest of the computer system with it. Jeremy is alerted to an activated tower and he, Aelita, Odd, Ulrich and Laura go to the lab to check it out. Laura's dad is called to the school as a result of the marks mix-up and he calls her back to the principal's office. He expresses his doubt in her abilities and his wish for her to go to another school. Laura insists on staying, deciding to show him the Supercomputer as proof of what she can do. Meanwhile, the others explore Lyoko looking for the activated tower that's nowhere to be found. Jeremy 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 Jeremy'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.
Enjoying their normal lives, Jeremy Belpois, Ulrich Stern, Odd Della Robbia, Yumi Ishiyama and Aelita Schaeffer soon discover that there is trouble still brewing at Kadic Academy. Even worse, the five best friends discover that their old and greatest virtual enemy - the evil, sentient and autonomous artificial intelligence/multi-agent system XANA - is somehow back and even stronger and more dangerous than ever before, as a highly evolved and modified version of itself. 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 war against XANA is far from over, and the five Lyoko Warriors are back in action.
The gang has planned a routine data gathering mission in the Cortex. However, Ulrich opts out of the mission when he finds out that Yumi wrote some negative things about him. While in the Cortex being attacked by Ninjas, Yumi can't stop thinking about Ulrich. She gets herself devirtualized on purpose just to go talk to him and work things out. The two soon reconcile. 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.
Towers are being activated and deactivated constantly. Laura follows the group and Jeremy allows her to help, seeing as it's an unusual case. While in the lab she asks Aelita about Franz Hopper. Not getting a decent answer, she goes to do research in the library before confronting Aelita, saying that she knows Franz built the Supercomputer, and that he apparently abandoned his daughter. Aelita replies that her father didn't abandon her, but that he sacrificed himself for her, and asks if Laura's father would do the same. Aelita returns to the lab. 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. Jeremy 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 tries to imprison Aelita and Yumi inside the Cortex, but Jeremy 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.
A man named Graven shows up at Kadic asking after Jeremy, the smartest kid in school, offering him a place in a special scientific institution specialising in quantum physics. Jeremy denies having any knowledge of the subject, then figures out that Graven is an agent sent by Tyron, and that they must have traced Lyoko's location on Earth somehow. Graven gives up on Jeremy and moves on to Laura, the second smartest in the school. 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 resists in the Digital Sea by sending Kongres, but they 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, asking her if she recognises 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. Jeremy 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.
Aelita dreams of her long-lost mother, Anthea. She wakes up and goes to see Jeremy, but finds Laura there with him, both working on the virus to destroy the Cortex. A hurt Aelita leaves, and Laura smugly denies that there was anyone at the door. Jeremy and Laura finish the virus and the group plans to implement it that afternoon, but Odd gets detention and Ulrich sprains his ankle, forcing both of them to opt out. William, Aelita and Yumi go in. 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 Jeremy what's going on, then moves to infect the Cortex with the virus. But then she looks up, and sees her mother 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 Jeremy 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. And assure her that if XANA gains too much power, they will destroy it and the Cortex immediately; no questions asked.
Thanks to Odd, Jeremy comes up with the idea of getting source codes back from specters, thus reducing and weakening XANA's strength and power greatly. The plan works, and they trap a specter, but things go horribly wrong when it ends up on Lyoko in the form of blackish-green particles, severely damaging and disabling the scanners and putting the Lyoko Warriors it touches into a coma-like state with black and green eyes. Jeremy 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 Jeremy 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 and find her mother. After the mission Jeremy 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 Jeremy 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.
A mission to gather more intelligence on Aelita's mother, Anthea, is cancelled when XANA launches another attack in the Mountain Sector. Unable to warn Odd and Ulrich, the two boys become the targets of XANA's attacks. Caught in the trap, Odd loses all of his codes once again. Meanwhile Aelita and Yumi are pinned in the Cortex by XANA's forces on route to deactivate the tower, and Yumi is later devirtualized. 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 co-ordinating with Odd, Odd is sent to provide William and Aelita with backup while Ulrich locates and escorts Yumi to the factory. After arguing with Jeremy over Yumi's safety, William devirtualizes himself in order to find her. Odd goes to Lyoko while Aelita is being perused by Kongers 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 Jeremy, Laura, and Aelita have been working on will now be used for destroying Tyron's supercomputer, and preventing any further communication with Anthea.
A tower is activated and a spectre is sent after Odd, taking the appearance of a football player. Aelita and Ulrich go to deactivate the tower, but when they reach it, Aelita is unable to enter. The tower deactivated itself because Odd lost the last of his source codes to the spectre. 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 realises 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. Meanwhile, William turns on his clone, allowing Yumi to get to the tower and deactivate it.
A new girl-genius and highly gifted teenage girl named Laura Gauthier tries to join the quintet at Kadic Academy. She humiliates Jeremy by correcting his mistakes on a complex exercise in class. Aelita suddenly is resentful and suspicious of this new girl, who seems to want to discover their secret. Meanwhile, Jeremy 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, Jeremy 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.
Aelita is determined to discover if her father really is involved in XANA's miraculous and mysterious return. So she, Odd, Ulrich and William go to the Cortex, with Odd piloting the Megapod to help her; as Yumi chose to stay behind to set up a fundraising party in the gym, enlisting the aid of a shy boy named Remi. He tries to help but accidentally breaks the sound system. Meanwhile, in the heart of the Cortex, the walls start to go haywire and devirtualizes Odd and Ulrich, leaving William to save Aelita before he, too, is devirtualized. Back on Earth, they go to help Yumi with the boy, who has been possessed by XANA. 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. Jeremy 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.
Jeremy is woken up by the Superscan when it picks up two activated towers. He warns the others, and just as they're leaving Aelita receives a message from an unknown sender asking her to meet them in a nearby building. While she's thinking about it, Laura comes and asks why she's not in class, then realizes that the others are at the factory. Aelita tells her to go on ahead, which she happily does. 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. Jeremy 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.
It's Friday the 13th and Odd can't believe his luck - he's won the lottery! He tries to impress Samantha with this fact, but he doesn't manage to catch up to her in time. Jeremy discovers that the lottery wins are happening all over Europe, and realises that it must be XANA. The group minus Odd head to Lyoko to deactivate the tower in Sector Five, which they do successfully. They return home and Odd comes to the lab feeling gloomy about not actually winning the lottery and his situation with Samantha, having bought a thousand red roses to give to her thinking he truly had won the jackpot. Jeremy 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. Jeremy 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.
Jeremy manages to develop a program that will allow the gang to hack Tyron's surveillance system and spy on him, both using video and sound, and potentially speak to Anthea. When the gang go to the Cortex to implement it, all but Aelita are devirtualized by Ninjas when they tip off an unforeseen security system. Aelita opts to stay in the Cortex's core to wait for her mother to appear, asking for a clone to replace her at the school while she's gone, which causes enough problems of its own. 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 very sad, but after Jeremy assures her that Anthea got the message, her spirits are rekindled.
While the Lyoko Warriors prepare to take advantage of a sunny afternoon, XANA launches an attack, sending them a polymorphic specter disguised as...them, constantly changing its appearance! Plus, not content with fighting unexpected specters at the school, our heroes are confronted with false avatars of themselves on Lyoko. Paranoia will soon settle in. And it's chaos on Lyoko as more false avatars keep showing up one after the other.
Laura and Jeremy finally finish their virus. Laura is keen to implement it immediately and destroy both the Cortex and XANA, but Jeremy insists they wait until Aelita has made more progress with her mother, Anthea. Meanwhile William has another argument with Ulrich. Laura takes the opportunity to try and recruit William for her cause, and after some persuading he hesitantly agrees. 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 Jeremy then kicked Laura out of the group and launched a return to the past to have her memory fully erased for defying him and the rest by acting on her own.
It's Aelita's birthday and someone is trying to hack into the supercomputer. The firewalls Jeremy created stop it from getting in. When analyzing the data packet sent, Jeremy notices that it is of unusual design; created by Franz Hopper. Perhaps Anthea is trying to contact them to wish her daughter a happy birthday. Jeremy calls the others but does not alert Aelita, as he wants it to be a surprise. 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 Jeremy 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. Jeremy loses all hope and begins to doubt his own abilities. Yumi goes to Lyoko to search for activated towers while Aelita and Jeremy work on fixing everything. After accidentally endangering Yumi's life, a depressed Jeremy leaves. Aelita saves her and then comes back to the lab to find Jeremy 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 Jeremy 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.
During a training mission on the Cortex, the Megapod bugs up and Jeremy is forced to figure out how to repair it. Just as he does so, the superscan finds an activated tower on the Cortex. But when they arrive on site, they find the tower has a purple halo. It has been activated by Tyron, and the Lyoko Warriors are soon surrounded by Ninjas, and Odd, Aelita and Ulrich become trapped in a temporal bubble that sends them back to that morning's gym class, repeating it dozens of times over. They must find a way to contact Jeremy to tell them what happened so that he can destroy the bubble before Tyron uses its signal to track their location on Earth. Meanwhile, Laura finds the card given to her in An Assured Professional Future. Not able to remember where she had gotten it from, she dials the number, arranging for a meeting via webcam. 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 Jeremy Belpois' friends. Tyron hangs up and thanks her greatly for her help, now intending to find Jeremy.
Our heroes are on the Cortex to inject Tyron's supercomputer with their virus. This should be their ultimate mission that will allow them to annihilate XANA. But it's a failure. They must wait twelve hours to be virtualized again, return to the Cortex and finish their mission. Only, an unpredictable event happens. Tyron goes to the school and proves himself to be the legal guardian of Aelita: he and Anthea have been married for four years. He gives her a terrible choice: find her mother again or infect his supercomputer. Aelita chooses to infect it, convinced that her mother would agree with her. Seeing things get away from him, and wanting to avoid the destruction of his supercomputer by a virus at all costs, Tyron decides to shut it down. Odd, William, Ulrich and Aelita, who were already on the inside, risk being thrown into the Digital Sea forever. Our heroes get out of it just in time and turn their own Supercomputer off, merely paralyzing XANA, not destroying it. Tyron becomes stuck: if he turns the computer on, the virus will activate and destroy his system. Despite this, the Lyoko Warriors have only won part of the battle. XANA and Tyron are both incapacitated, yet 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 ever, the Warriors must remain on their guard as they begin a new battle: the one to keep their family together.
William is yet again rejected by the group, but when he asks Yumi for her help on a project she happily agrees, much to Ulrich's disdain. The dislike between the two grows when XANA creates a spectre of William to attack Yumi, and the two almost have a fistfight in the gym. 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.