Realizing the danger the supercomputer represents, Jeremie takes the advice of his three new friends and decides to shut it down, but not before materializing Maya (Aelita) into the real world. Meanwhile, the strange events become a consistent problem when an electric orb begins hunting Jeremie and his friends. When the orb attacks Ulrich and Yumi a stubborn Yumi demands to know what is going on, forcing Ulrich to take her to the supercomputer with him. In a trip to Lyoko, Ulrich, Odd and a newly recruited Yumi work together to get Maya to the red tower under the assumption that it will bring her to the real world. This assumption is ultimately false, neutralizing the attack on Earth rather than materializing her.
Jeremie then discovers another sentient being, an evil, rogue artificial intelligence/multi-agent system called "X.A.N.A.", which is causing the attacks in the real world by activating the towers on Lyoko in order to rule humanity. Maya (who discovers her real name is Aelita when deactivating the tower) suggests they shut down the supercomputer, but the group decides to help Jeremie until Aelita is successfully materialized into the real world. Thus, the Lyoko Warriors are born.
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 Ulrich and Odd return to Earth if they are killed on Lyoko, but she'd disappear if she is. 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 he will—right after he materializes Maya. Sissi heads for cheer leading 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 Roachsters and a pair of Hornets. While all of this is happening, Ulrich returns to the gym and engages in a rematch with the Japanese girl. In the end, they call a draw and the girl introduces herself as Yumi. 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-chemestry report while christening him with the nickname "Einstein".
Sissi, meanwhile, fails her cheer-leading 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 slit up with Yumi 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; she holds him back unless he agrees to let her in on whatever is going on. Given the gravity of the situation, the team agrees and Yumi is taken to the factory. She agrees to be virtualized on Ulrich's dare, despite not believing their story at first, and the three manage to rescue Maya in time. 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 crab-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 not the 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.
- Had this two-part prequel been added to the first season, it would have consisted of 28 episodes.
- It is shown that if someone jump off of land in the Mountain Sector, they fall back on land in another place, but still in the same sector.
- This is the first and only two part episode of Code Lyoko. Officially; Other episodes are seemingly two parted just not named as such (e.g. Code: Earth with False Start).
- Part 2 shows us that Yumi was first virtualized into the Ice sector. The only others not virtualized onto the Forest sector first are William and possibly Jeremie.
- At one point in Part 2, Jim mentions a giant, chemical teddy bear. Later in Teddygozilla, he attacked by a giant teddy bear.
- After a brief match in the gym, Ulrich mistakenly calls Yumi "Yuri", to which she replied to with instantly knocking him down, since Yuri is an anime genre involving romance between women. It's likely Yumi knew what "Yuri" meant.
- Yumi did not use her telekinesis, probably because she does not she possess it.
- Ulrich never used his three special abilities of super sprint, triplicate or triangulate.
- The Desert and Mountain regions are not seen.
- The Ice Sector was the first region where Yumi was virtualized for the first time.
- This is is actually the very first time that the Return to the Past function was discovered and used.
- X.A.N.A.'s very first attack (after being inadvertently reactivated by Jeremy activating the supercomputer) was an orb of extremely powerful electrical energy.
- Odd is seen utilizing his purple shield ability in the Ice Sector, even though it does not appear until Season 2.
- The activated tower is red, in a scene later on, it turns back blue and then turns red again.