Code Lyoko Evolution

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.

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.

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 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 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.

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.

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.

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.