This episode continues where Part 1 left off. The next morning, Odd greets Ulrich and Sissi over breakfast, revealing he had styled his hair in a spiked-up fashion similar to his virtual look. Meanwhile, Jeremie is on his computer, furthering his research on Lyoko. He explains to Maya that while Ulrich and Odd return to Earth if they are killed on Lyoko, she will disappear forever if she were. But, on the bright side, Jeremie discovers that the towers serve as portals between Earth and Lyoko and believes that the red tower discovered in the Ice Sector, as the red color signifies activation, could be used to materialize her.
However, the other three in on the secret aren't too keen on the idea, believing the monsters there would pose too much of a problem. Ulrich still insists on shutting the computer down, and Jeremie promises that he will, right after he materializes Maya. Sissi heads for cheerleading practice and invites Ulrich to watch, but he claims to have business to take care of. As Sissi heads confidently to her audition, an electrical orb emerges from the outlet next to her dorm.
Meanwhile, on Lyoko, a strange pulse radiates from the activated tower and is heard by Maya in the Forest Sector. She calls to Jeremie, but when he doesn't answer, she sets off on her own. She makes it to a mountain-like terrain before she is attacked by more monsters, including the Kankrelats and a pair of Hornets.
During all of this, Ulrich returns to the gym to have a rematch with Yumi Ishiyama, his sparring partner in his martial arts class who had beaten him. In the end, they call a draw and formally introduce themselves to each other. Jeremie and Odd head to the library where Jeremie researches a program called "Return to the Past". Odd asks Jeremie for help on an electro-chemistry report while christening him with the nickname "Einstein".
Sissi, meanwhile, fails her cheerleading audition miserably and returns to her dorm in a foul mood. Once alone, she is attacked by the electrical orb and rendered unconscious. The orb vanishes just as Nicholas Poliakoff and Herb Pichon find Sissi in her condition. When they try telling Principal Delmas about the incident after taking her to the infirmary, he doesn't believe them but Jeremie and Odd become suspicious. Back at the gym, Ulrich is just about to leave Yumi following their rematch and return to his friends (and learns she has none) when the same electrical orb from before emerges from the lights and attacks them both.
Over their cell phones, Ulrich agrees to meet Jeremie and Odd at the factory to help Maya, but says a little too much around Yumi. Suspicious of the strange events unfolding around her, she holds him back and insists on being told what is going on. Given the gravity of the situation, the team agrees and Yumi is taken to the factory with them. She agrees to be virtualized upon a dare by Ulrich, despite having difficulty believing their story at first, and the three manage to rescue Maya in time in the Ice Sector. Yumi discovers her weapon is a frizbee-like fan that slices through monsters when thrown.
At the infirmary, Sissi wakes up and, in a panic, forgets her word of secrecy and blabs the entire secret to her father and Jim. They don't believe her story, so she takes them to the factory to prove herself. While she does, the electrical orb attacks Jeremie in the lab and the group on Lyoko are attacked by two krab-like creatures on their way to the red tower. They manage to kill one of the monsters before Odd and Ulrich are devirtualized, and Maya blocks off the remaining one by instinctively materializing a wall of ice. Yumi watches Maya make it to the tower just before being devirtualized herself.
When Maya enters the tower, a floating screen appears, giving her a little scare, she touches a floating screen that spelled out a name she seems to recognize: "Aelita". It then spells out the words "Code: Lyoko", and the electrical orb vanishes. But Jeremie and the others aren't out of hot water yet, as they are now in trouble with the principal. Ulrich spurns Sissi for breaking her oath, but she retaliates, pointing out that Ulrich brought Yumi in. With no other option, Jeremie launches the "Return to the Past" program to escape having to shut the supercomputer down.
The next thing Ulrich, Odd, and Yumi know, it's a day earlier - around the same time Jeremie had been electrocuted by the vending machine. However, it seems Jeremie remembers nothing of the incident or anything that happened since. After the three explain everything that had happened, Yumi concludes that only those who'd been scanned by the supercomputer can remember. Maya insists that the supercomputer be shut down anyway, believing it to be too dangerous. She also reveals that her name is actually Aelita, which she remembered when seeing it on the interface in the tower. Jeremie continues looking into materializing her for another night anyway and eventually figures out that the artificial intelligence that had been attacking them was named X.A.N.A. and had been using the red tower to launch his attack.
Ultimately the gang decides to not shut down the supercomputer, now that they know how to counter X.A.N.A.'s attacks, and Jeremie will continue to hunt for a way to bring Aelita into the real world. The gang voice a vow of secrecy which they truly intend to keep, and their virtual adventures begin.
- The original French names for Part 2 is Le réveil de X.A.N.A. partie 2.
- In Finland, this prequel premiered before Season 2.
- It is revealed in this episode that if someone jumps off of the land in the Mountain Sector, they fall back on another place in the same sector.
- This is the first and only two-part episode of Code Lyoko. Officially, other episodes are seemingly two parted, but are not named as such (e.g. Code: Earth with False Start).
- This part of the prequel reveals that Yumi was first virtualized onto the Ice Sector; this means that the only other Lyoko Warriors who were not first virtualized onto the Forest Sector are William, who was first sent to Sector Five, and possibly Jeremie, whose first sector remains unknown.
- In the infirmary, Jim mentions a giant, chemical teddy bear, which foreshadows the events of Teddygozilla, where he is attacked by a giant teddy bear possessed by X.A.N.A..
- Yumi did not use her Telekinesis, nor did Ulrich use his two special abilities of Triplicate or Triangulate in this episode, probably because they don't know they possess them yet.
- This episode reveals that Aelita does not need to type in the word "LYOKO" in order to deactivate a tower. Instead, it automatically appears when she interacts with the screen.
- The Desert Sector was the only surface sector that wasn't visited in either parts of the prequel.
- The Megatank is the only monster of the original group (Kankrelats, Krabs, Bloks, Hornets, and Megatanks) that was not seen in the prequel.
- This is the very first time that the return to the past program was discovered and used by the group.
- X.A.N.A.'s very first attack (after being inadvertently reactivated by Jeremie restarting the supercomputer) was revealed in this episode to be an orb of extremely powerful electrical energy.
- The tower activated in this episode is the same tower X.A.N.A. would eventually activate in Guided Missile.
- When Aelita jumps into the void in the way tower of the Mountain Sector, the tower she exits through in the Ice Sector is shown to be white instead of blue, and then its halo changes from white to red when Aelita starts to run away from the Bloks that were waiting for her.
- During Odd's first trip to Lyoko in Part 1, his avatar's design is already fully shown on the interface even as he is being virtualized. During Yumi's first trip, however, a blank image is shown.
- In one scene, the activated tower goes from red to blue, and then back to red.
- When Jeremie tells everyone that more monsters were coming from the tower, he was wearing his headset, but in the next shot his headset was missing.
- While Yumi is fighting one of the Krabs, and while it is firing at her, its laser is not shown.
- In Part 1, Jeremie pressed the number 6 button on the vending machine, but after the return to the past, he pressed the number 7 button instead.