The episode opens during gym class, the class are picking teams and Jeremy is picked last (as usual). Upset, Jeremy runs out of the gym with Odd and Ulrich following him. Outside the gym, Odd and Ulrich try to cheer Jeremy up however he sulks away. Later, in his room, Jeremy is scanning Lyoko for X.A.N.A.-Sissi or an activated tower before he gets angry at himself for hoping for an X.A.N.A. attack. A few moments later, Aelita enters the room and asks if he was alright after hearing the story from Odd and Ulrich. Jeremy however shouts at her stating that she had fun on Lyoko while he stayed sitting in his chair, the four-eyed know it all, realising what he had just said, he leaves with Aelita standing stunned. Meanwhile X.A.N.A activates a tower in Xanadu.
In the Factory, Jeremy is sitting in one of the scanners, angry with himself for shouting at Aelita and for losing his temper with Odd and Ulrich. In the Lab above a rat is on top of the computer interface when a spectre possesses it with X.A.N.A. The rat begins to attack the cables on the keyboards, this causes the scanner that Jeremy is sitting in to activate and virtualize Jeremy. Jeremy lands unconscious in a new sector of Xanadu.
At Kadic, Aelita meets up with Odd and Ulrich, she asks about Jeremy however they said she couldn't find him. Yumi then arrives and states that she had looked everywhere for Jeremy, Ulrich then suggests that they go and search Jeremy's room. When they arrive, they find the room empty and as they begin to wonder where he went, Aelita spots that the Superscan has located an activated tower, the team conclude that Jeremy must be at the factory.
In Xanadu, Jeremy is in a sector which it appears to be the sector 5, but then turns all red because he are in the sector that Lyoko-Warriors discovered in "Xanadu, Part 2". There X.A.N.A.-Sissi appears, using the pink spirit, knocks Jeremy and take him to another room to throw him into the Digital Sea. Then Jeremy wakes up and he sees a Tarantula, a Kankrelat and a Blok watching them.
At the factory, Odd, Ulrich, Yumi and Aelita arrive at the Lab to find the door jammed (as the rat had chewed the cables). Meanwhile X.A.N.A.-Sissi begins to attack Jeremy when the group of monsters attack Jeremy too. In the lab, Odd and Ulrich manage to force the doors open and take care of the rat. On Lyoko, X.A.N.A.-Sissi easily surrounds Jeremy, just as she is about to attack him, Aelita's voice calls out. Jeremy hurriedly replies and Aelita realises that he is on Lyoko and as he had been virtualized by a rat.
Aelita quickly virtualizes Odd, Ulrich, and Yumi to Xanadu (she can virtualize them directly because Jeremy is in Xanadu), Jeremy tells Odd to devirtualize him so he can return to the Lab, Odd quickly devirtualizes him while Yumi and Ulrich attack X.A.N.A.-Sissi. Jeremy quickly takes his position in the lab and Aelita heads for the Scanner Room. On Lyoko, Ulrich is dueling X.A.N.A.-Sissi however he looses and gets devirtualized, Yumi continues to attack with her fans. Jeremy virtualizes Aelita, while X.A.N.A.-Sissi spots this and hurls his blade at her, Yumi however takes the blade and is devirtualized, to X.A.N.A.-Sissi's fury.
X.A.N.A.-Sissi, infuriated by his defeat, dives into the Digital Sea, swearing revenge. Jeremy then launches the return to the past. It's gym class and the class is playing basketball, in the end although Jeremy's team lost the match Odd, Ulrich, and Jeremy all laugh much to Jim's confusion.