In the cafeteria, Odd and Aelita play with their food by flinging it into the air on the backs of their forks. Eventually, the William Clone begins imitating them from another table, and flings a glass into the air. Jim catches the glass, berates the Clone, and gives it detention. The Lyoko Warriors then discusses the William Clone, and Jeremie explains worriedly that it is not supposed to have the ability to take personal initiatives, and thus should not have tried to imitate Odd. Jeremie also mentions that he installed an upgrade the day before to try and make the Clone "less stupid", and that he may have to delete the upgrade if the Clone continues to act out.
After lunch, Jeremie announces more news in the courtyard: he has modified the Superscan program so that it may detect Replikas on the Network, and he has already managed to locate a new one. After making plans to explore the Replika that evening, Aelita expresses regret over having gotten the Clone into trouble. Jeremie then reminds her that, as a program, the Clone as no feelings, and the group disperses to go to their afternoon classes. However, it is revealed that Milly and Tamiya have been eavesdropping on the Lyoko Warriors' conversation, and now know that the William at school is actually "an artificial clone".
Once classes let out, the William Clone serves its detention in the campus library with Jim while the group travels to the Factory. There, Aelita, Odd, Yumi, and Ulrich are sent to Lyoko and board the Skid. Aelita then pilots the ship out of Lyoko and into the Digital Sea, where she travels to the new Replika. Meanwhile, on campus, the William Clone finishes its detention and is approached by Milly and Tamiya. Under the pretense of doing a report on school punishment, the girls attempt to learn more about "William" and his status as a clone.
The Skid arrives on the Replika, which is revealed to be a copy of the Desert Sector, and Aelita docks the ship to a tower. Jeremie then activates the tower and uses it to translate Aelita and Ulrich to Earth while Yumi and Odd stay behind to guard the Skid. In the dormitory building, Milly and Tamiya continue to interrogate the William Clone until, unaware it is supposed to keep the information secret, it reveals to them that it is not the real William, confirming the girls' suspicions.
Meanwhile, Ulrich and Aelita arrive at an abandoned military facility somewhere in the New Mexican desert. As they navigate through the building, Yumi and Odd are confronted by several Hornets on the Replika, and a battle breaks out in front of Jeremie's tower. In William's dorm room, the Clone tells Milly and Tamiya about X.A.N.A., Lyoko, and the Supercomputer. When they ask for proof, the Clone offers to take them to the Factory.
While Jeremie virtualizes vehicles for Odd and Yumi, he is alerted to activity in the Scanner Room, and it is revealed that the real William, still possessed by X.A.N.A., has returned to Earth. Jeremie watches security camera footage of William going down to the Supercomputer Room, and leaves the Lab to confront him. On the Replika, Yumi and Odd defeat the Hornets, but are forced back into battle shortly afterward when three Tarantulas appear at their position.
Jeremie arrives in the Supercomputer Room armed with a metal pipe, but is quickly dispatched by the superpowered William. Meanwhile, in New Mexico, Ulrich and Aelita find an automated assembly line manufacturing circuit boards, and Aelita begins to worry when she notices they have lost contact with Jeremie. As Aelita and Ulrich discuss whether or not to abort their mission, Milly, Tamiya, and the William Clone arrive at the Factory and find Jeremie at the mercy of the real William. The Clone advances on William to defend Jeremie, and the two clash violently. Jeremie, whose ankle has been injured, asks Tamiya to go up to the Lab and relay information to the others.
On the Replika, Yumi and Odd battle the Tarantulas until Tamiya arrives at the interface and tells them to "come back right away". Aelita and Ulrich hear the instructions and well, and knock each other out, forcing them both back to the Skid. Yumi and Odd continue to fight until Yumi is devirtualized by a Tarantula. Once she wakes up, Aelita manages to energize Odd back into the ship and detach from the tower. The Skid then leaves the Replika and begins the return trip back to to Lyoko.
Meanwhile, during their struggle, the Clone hurls William into the elevator, which goes up to the Lab. Tamiya, thinking he is the "good guy", relinquishes control of the interface to William, who then attacks her before shutting down the Scanners with Yumi still inside one of them. When the Clone arrives in the Lab, William deletes it with a few keystrokes before tampering with the Supercomputer's cooling system. Down in the Supercomputer Room, Jeremie and Milly watch as the server begins to overheat, and Jeremie asks Milly to go up to the Lab to confront William.
Meanwhile, in the Digital Sea, the Skid is attacked by two Sharks, and Aelita releases Odd and Ulrich's Skids to engage them. Yumi finally manages to pry her Scanner doors open as Odd and Ulrich defeat the monsters. As Milly arrives in the Lab and begins shouting empty threats at William, Aelita rushes back to Lyoko and docks the Skid in its hangar. Ignoring Milly, William finishes sabotaging the cooling system and sets up a delayed virtualization for himself.
Ulrich, Odd, and Aelita devirtualize one another in the hangar, and the three of them and Yumi go up to the Lab together to confront William. However, William has already returned to the Scanner Room using an emergency ladder and escapes back onto Lyoko. Aelita then takes control of the interface, and manages to repair William's damage, saving the Supercomputer. Once the chaos dies down, the Lyoko Warriors humor Milly and Tamiya by giving a full-disclosure interview about Lyoko before Jeremie performs a Time Reversion, wiping their memories, healing Jeremie's ankle, and restoring the William Clone.
Back in the cafeteria, Odd refrains from flinging his food again, worried about how the Clone may react. Jeremie then reveals to the others that the upgrade he gave the Clone was actually a preexisting program Franz Hopper had made, and postulates that the program was instrumental in the creation of X.A.N.A.'s tyrannical personality. Jeremie vows to create a new, less dangerous program, and as he looks over at the Clone, it smiles back at him.
- The original French name of this episode is Œil pour œil, which translates to "Eye for an Eye".
- Sharks make their debut in this episode.
- Jim's weight is revealed to be roughly 240 pounds in this episode.
- This episode marks the first time Jeremy did not use the enter key to perform a Time Reversion.
- This episode marks the first time Milly and Tamiya have been inside the Lab.
- Yumi used her stronger telekinesis to get back Odd's Overboard.
- William is shown wearing his season four clothing. However, he was virtualized onto Lyoko wearing a different outfit, and there is no way he could have changed clothes while on Lyoko.
- When Aelita arrives at the Lab to fix the Supercomputer's cooling system, she does not put the earpiece on when she sits down. However, in the next shot, she is shown wearing the earpiece.