|"Aelita, we've done it. X.A.N.A.'s been destroyed."|
In a vivid nightmare, Aelita has a premonition about the death of her father, causing her to wake up screaming. In the morning, Aelita goes to visit Jeremie in his dorm room, where it is revealed that he has been up all night working of his multi agent program. Aelita worries about Jeremie's unhealthy sleeping and eating habits before going to breakfast without him. In the cafeteria, Aelita tells Yumi, Ulrich, and Odd about her nightmare, but they reassure her that everything will be fine. William then arrives and asks to sit with them. However, after an unintentionally cold greeting, William is hurt, and goes to sit alone. Aelita then scolds the others for still treating William like an enemy, and Ulrich, Odd, and Yumi agree to be fairer and more civil with him, but assert that he should no longer be allowed in the Factory.
Meanwhile, as he continues to work in his dorm, Jeremie receives a message from Franz Hopper, who asks for a meeting. Excited, Jeremie calls to inform Aelita before traveling to the Factory, and she and the others leave the cafeteria to go to the Factory as well. In the park, Sissi sits alone, listening to music until she notices Jeremie running into the trees. Curious, Sissi decides to follow him, but loses him once he enters the manhole into the sewers. When Ulrich, Yumi, Odd, and Aelita arrive at the manhole shortly afterward, Sissi demands to know where they are going. As the four lie, claiming to be going to the gym, Jeremie arrives at the Factory and calls Aelita, telling her to hurry.
After finding the sewer door in the school is locked, Aelita, Yumi, Odd, and Ulrich are confronted again by Sissi. However, William then arrives and begins flirting with her, allowing the others to escape while Sissi is distracted. After they finally reach the Lab, Jeremie tells the others that Franz Hopper has sent him coordinates to a rendezvous point in the Ice Sector. Although they do not know what Hopper is planning, Jeremie instructs the others to protect him from X.A.N.A.'s monsters. However, William then arrives and asks to go on the mission as well. Yumi refuses, seeing William more as a liability than an asset, but Jeremie makes a compromise: William will stay in the Lab on standby, and will only be sent to Lyoko as backup.
Ulrich, Odd, Yumi, and Aelita are then sent in the Ice Sector, where Jeremie directs them to a cave entrance hidden by a waterfall. Aelita asks the other if she may have a moment alone with her father, and enters the cave by herself, finding Franz Hopper waiting for her inside. However, Jeremie is then alerted to an activated tower, and before he can warn the others, a spectre emerges from wiring in the walls and possesses William. William then attacks Jeremie, knocking him unconscious before heading to the Scanner Room.
As Aelita notices Jeremie has stopped responding to her, she and her father exit the cave to find the Kolossus and a swarm of Mantas have arrive at their position. Deducing that something has gone wrong at the Factory, Yumi volunteers to be devirtualized by the Kolossus in order to return to Earth, where she finds William in the process of destroying the Scanners. As Ulrich attempts to battle the Kolossus, Odd and Aelita escort Franz Hopper to safety, fending off the Mantas along the way. In the Scanner Room, Yumi is quickly outmatched by the superpowered William, and tries in vein to flee into the elevator. However, William phases through the elevator door and attacks Yumi, throwing her out once they reach the main floor.
In the Lab, Jeremie regains consciousness, and discovers that Hopper is in the process of sending him data. As Yumi struggles against William, Ulrich reaches the Kolossus's head and damages one of its weak points, temporarily immobilizing it. Hopper then abruptly returns to the Digital Sea after sending Jeremie the data necessary to turn his multi agent system into an "anti-X.A.N.A. program". After perfecting the program, Jeremie then informs Aelita that she must go to Carthage to help him launch it. As Ulrich defeats the Kolossus, Jeremie inputs the Scipio code and sends Aelita and Odd to Sector Five. Ulrich is then crushed by the falling Kolossus and is devirtualized.
In Carthage, Aelita and Odd enter the Celestial Dome, where Aelita attempts to launch the anti-X.A.N.A. program, but quickly discovers the Supercomputer does not have enough power to run it. The pair is then attacked by Mantas, and Odd is devirtualized. In the Factory, Yumi and William's skirmish spills into the assembly room, where Yumi is injured. However, Ulrich soon comes to her aid, and takes over battling William until he too is injured.
On Lyoko, Franz Hopper reappears in the Celestial Dome with Aelita, and begins sending power to the supercomputer. However, Aelita's premonition comes true as the Mantas begin attacking her father, rapidly depleting his life points. Now with enough power, Jeremie instructs her to launch the program, but Aelita instead tries desperately to save her father from the monsters. In an emotional argument, Jeremie eventually convinces Aelita not to let Hopper's sacrifice be in vein, and she launches the program just as her father is killed.
The anti-X.A.N.A. program is a success, and X.A.N.A. is destroyed. In the Lab, Jeremie watches the interface in amazement as his program causes all the Replikas on the internet to vanish. In the assembly room, Yumi and Ulrich look on as a massive spectre is forced out of William's body and disappears. Jeremie then manually devirtualizes Aelita, and all five Lyoko Warriors convene in the Scanner Room, where Aelita, distraught over the loss of her father, cries into Jeremie arms.
- The original French name for this episode is Contre-attaque, which translates to Counterattack.
- The Kolossus is defeated for the first and only time in this episode.
- Franz Hopper is killed in this episode, making his the only character death in the series and the only known casualty in the war against X.A.N.A.
- In the park, Sissi was listening to Break Away by the Subdigitals, the song that is played during the end credits of every episode since the start of season two.
- Jeremie claims to have finished the multi agent program just before he is contacted by Franz Hopper. However, after Franz Hopper sends him vital data, he claims the program is incomplete without said data.
- When Jeremie enters the manhole in the park, he is briefly shown wearing his outfit from seasons one through three as opposed to his current outfit.