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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.

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.

When a kid goes up to hug Aelita, he leaves and comes back and does the same to Yumi. Jeremy immediately realizes that XANA has sent a specter to retrieve the codes it implanted into four of its greatest enemies to regain its full strength and power. So they go to Lyoko and attempt to deactivate the tower in the Desert sector while Odd stays at the school to hold it off, but the situation escalates when Aelita gets hit and is devirtualized. She guides Yumi from Earth, supposing that XANA's source codes can allow the others to deactivate towers. Her theory is correct and Yumi deactivates the tower, only to reveal another one masked by the first's signal; another spectre is somewhere on Earth.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.