It is nearing the end of the semester at Kadic Academy. Aelita, Yumi, Odd, and Ulrich enter the Lab to find Jeremie watching videos from Franz Hopper's diary that document his discovery of the Supercomputer's Time Reversion function, and how he relived June 6, 1994 at least 2,546 times and became mentally unhinged. Jeremie shows the others a specific video in which Hopper explains his plan to send himself and his daughter, Aelita, to Lyoko, where they will each hold a set of "keys to Lyoko" and live forever. Jeremie deduces that these "keys" are what X.A.N.A. wants from Aelita, and Aelita herself concludes that, with them, X.A.N.A. would be able to escape from the Supercomputer.
Later, during breakfast in the school cafeteria, Jeremie reveals more news: X.A.N.A. did not give Aelita a virus, as was previously thought, but rather took something from her, a "fragment", which Jeremie has located inside Carthage. Odd suggests they retrieve the fragment that night, after the End of the Year dance, as their final mission. However, Aelita, who had been in a noticeably bad mood throughout the conversation, refuses to participate in the mission and storms out of the room. Jeremie follows her outside, and Aelita tells him about her new-found resentment toward her father, how she feels he stole her childhood by bringing her to Lyoko, and that she never wants to go to Lyoko again. Jeremie tries to reassure her that everything be fine once they retrieve the fragment, but Aelita's bad mood persists, and she walks off again.
Meanwhile, in the courtyard, many students try to find dates for the dance. Yumi attempts to ask Ulrich to be her date, but William distracts her with a proposal of his own, which she rejects. Ulrich sees them talking, assumes Yumi has agreed to go with William, and feels hurt and vindictive. So, when Sissi approaches Ulrich, he accepted her offer solely to get back at Yumi.
Unbeknownst to anyone, Aelita travels the Factory, where she enters the room housing the Supercomputer and shuts it down, causing her to lose consciousness and collapse. A short time later, Jeremie discovers the Supercomputer is unresponsive, prompting him to go to the Factory to fix the problem. When Yumi discovers Ulrich has agreed to go with Sissi out of spite, the two friends quarrel, leaving Yumi hurt and Ulrich ashamed of himself.
Jeremie arrives at the Lab and finds the interface display blank. He then goes down to the Supercomputer room to check for problems, where he finds Aelita's body and the powered down Supercomputer. He hurriedly reboots the Supercomputer, and Aelita regains consciousness. She explains that she was willing to sacrifice herself to save the rest of the world, but Jeremie reassures her they can save the world together.
That evening, Ulrich decides to stand Sissi up and instead goes to Yumi's house to apologize. Before he actually says anything, however, he is interrupted by a call from Jeremie, who asks him and Yumi to come to the Factory. Yumi accepts Ulrich's unspoken apology, and the pair reconcile. Ulrich then calls Odd, who has failed to find a date due to his promiscuous reputation, and the three set off for the Factory together.
Odd, Ulrich, Yumi, and Aelita are virtualized onto the Ice Sector before Jeremie enters the Scipio code and the Transport Orb arrives to take them to Carthage. In the Core Zone, a countdown starts and seven Creepers appear. Odd and Ulrich battle the Creepers while Yumi scales a large wall to reach the Key Mechanism. Once the Creepers are defeated, Yumi presses the mechanism, and the floor transforms into a downward-spiraling staircase, which the group descends.
At the bottom of the staircase, they find a long, narrow bridge, at the other end of which is Aelita's missing fragment. As they begin to run down the path, they are confronted by several Creepers. Odd, Yumi, and Ulrich stay behind to hold the monsters off while Aelita attempts to reach the fragment, but she is stopped when she finds a large gap in the bridge. Yumi and Ulrich rush to Aelita's aid, and Odd stays behind to fend off the monsters. Odd is overwhelmed and devirtualized while Yumi and Ulrich work together to throw Aelita to the other side of the gap. Aelita makes it across, but Ulrich and Yumi are left dangling over the gap. The Creepers catch up to them and open fire. Yumi is devirtualized, but Ulrich manages to climb up and defend himself.
The bridge then begins to collapse, and Ulrich and Aelita fall. However, their fall is broken by two Mantas, revealed to be under the control of Franz Hopper. The Mantas fly Aelita and Ulrich over to the platform with the fragment, and Aelita takes hold of it. It is then revealed that the fragment is a fake, a trap set by X.A.N.A., and the entire room begins to fall apart. Ulrich and the Mantas are crushed by falling debris, leaving Aelita trapped on a platform in the center of the large room.
The Scyphozoa arrives and begins to drain Aelita's memory. With no one to save her, the Scyphozoa succeeds. Aelita falls to the floor, presumably dead, as the light starts to fade from Carthage and Lyoko itself begins to shut down. All across Lyoko, the towers turn red, and X.A.N.A., now possessing a set of Keys to Lyoko, finally escapes from the Supercomputer.
Suddenly, a white light envelops Aelita's lifeless body, and she has multiple visions of her childhood on Earth before regaining consciousness. The light returns to Carthage, and Lyoko's towers turn from red to white. It is revealed by Jeremie that Franz Hopper has used his own Keys to Lyoko to restore the virtual world, and that he has given Aelita back her missing fragment, which is discovered to be the memories of her past life. Jeremie manually devirtualizes Aelita, and he, Odd, Ulrich, and Yumi rush down to the Scanner Room to greet her, where faints once again, this time in Jeremie's arms.
Later that night, all five Lyoko Warriors sit in Jeremie's dorm room. Aelita expresses a desire to find her father, who seems to have disappeared from Lyoko. They also discuss how Aelita is no longer tethered to Lyoko, but that X.A.N.A. no longer is, either, and that shutting down the Supercomputer now will do nothing to stop him. Jeremie concludes that they must continue the fight, and he also promises to look for Franz Hopper. The rest of the group makes similar promises as they all hold hand with one another in solidarity.
- The original French name for this episode is Réminiscence.
- The revelation that Aelita does not have a virus creates a continuity error; if Aelita did not really have a virus, the Marabounta should not have targeted her in episode 36.
- This episode originally aired as a double bill with Revelation.
- From this episode onward, neutral, deactivated towers glow white as opposed to blue. This is because Lyoko now runs using Franz Hopper's Keys; Hopper used to turn towers white when he would activate them.
- It is revealed in this episode that Franz Hopper created X.A.N.A to destroy "Project Carthage". It is unknown what that means or if this task was ever accomplished.
- This episode marks the first appearance of Aelita's mother, which shows that Aelita's bright pink hair is inherited.
- Franz Hopper's possession of Mantas marks to only time in the series someone other than X.A.N.A. controls Monsters.
- In the flashback in which Aelita and Franz Hopper are in the sewers, Aelita's voice briefly changes from a younger voice to her normal voice. It is unknown whether or not this is an error.
- Yumi's farewell clip in Echoes is taken from this episode.
- Franz Hopper relives June 6, 1994 2546 times, which adds up to 6 years and 356 days.