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.