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.

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.

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