The episode begins with Odd finding Ulrich in the bathroom brushing his teeth. Odd asks him what he wants for breakfast and leaves to go get something to eat. Ulrich then sees a spectre taking his appearance before abruptly vanishing. That morning, Yumi is telling the group of the same thing happening to her at home. Jeremie adds that towers are being activated and are randomly deactivated constantly and is unsure if it's a X.A.N.A. attack or not. They decide to go the Lab to figure things out, but Yumi and William say they can't go as they have a test.
As Jeremie, Aelita, Odd and Ulrich go to the Factory, Laura follows the group, asking what they are doing. Aelita clearly doesn't want her to come along, but Jeremie allows her to help, seeing as it's an unusual case much to Aelita's disdain. In the Lab, Ulrich and Odd are sent to deactivate two towers that keep being activated and deactivating over and over. While on the mission, Odd brings up Franz Hopper and mentions how he is Aelita's father. Laura, confused since she doesn't know much, asks Aelita about Franz while bringing up how the two didn't share the same last name despite the relation between them. Aelita snaps at her to "mind her own business" before turning her attention back to the mission. Yumi and William then come to the scene, having been sent a text by Aelita to come help. Jeremie then sends the group (excluding Aelita) to the Cortex for answers. Laura then leaves, claiming to have homework she's behind on.
On Lyoko, the group goes to the Cortex while Aelita leaves as well saying she has something to "check up". While the group is on the Skid travelling to the Cortex, Aelita spies on Laura who is at the school's library. As Laura leaves to look for a book, Aelita looks at her tablet to see that she is researching information on her father. She then leaves when seeing Laura coming back. However, she is soon confronted by Laura, who saw her look at her tablet, as she leaves. Laura tells Aelita that she knows Franz built the Supercomputer as well as Lyoko. At first, Aelita tries to deny everything, but Laura asks why he suddenly disappeared and if he abandoned her, choosing his research over his daughter. Aelita replies that her father didn't abandon her, but that he sacrificed himself for her and remarks if Laura's father would do the same, before she returns to the Lab.
While on the Cortex, the gang stumbles upon a Krab and Ninja fighting each other at the Core's entrance. Much to their confusion as X.A.N.A. gained its network access through Tyron. The Krab defeats the Ninja and Jeremie tells them to follow the Krab inside as it goes inside the Cortex, needing to know what is going on. The group then carefully go inside the Cortex to find a huge battle between Tyron's Ninjas and X.A.N.A.'s monsters in the Dome, and can't figure out why the two are fighting each other. Jeremie and Aelita contemplate X.A.N.A. must have a reason for all of this just as the group is noticed, resulting in a Krab taking out Yumi. Ulrich, Odd and William then battle both the Krabs and Tarantulas as well as the Ninjas. During the battle, both William and Odd are devirtualized by the Ninjas and Ulrich is left to gather information on his own.
After downloading the data, the group learns that X.A.N.A. destroyed a security update by Tyron on his supercomputer, the update being the source of the interferences of X.A.N.A.'s attacks. They then guess that Tyron possibly doesn't know that X.A.N.A. is living inside his Supercomputer and decide to warn him. Jeremie then decide to organize a meeting with Tyron and sends him a request for one.
Later that night, Jeremie receives a message from Tyron, accepting his offer for a meeting. He calls Ulrich to tell the rest of the gang to meet at the factory. As they travel to the factory, Jeremie decides to have Aelita and Yumi attend the meeting with Tyron, much to the contemplation of the boys who are concerned for them safety wise. However, Jeremie is firm on his decision, and Aelita and Yumi are sent to talk to Tyron about X.A.N.A. in the Cortex. In the Cortex, the girls have the meeting with Tyron in a Skype-like video chat. Tyron claims he knows nothing about the artificial intelligence/multi-agent system, and that there was no way it could be living inside his supercomputer as he would know about it. Aelita tries to reason with him that X.A.N.A. is nearly out of control and will wreck havoc and destruction, but Tyron firmly states that he fears no one.
Tyron then tries to imprison Aelita and Yumi inside the Cortex by using two Ninjas that were hidden, but Jeremie pulls them out just in time. It's then that the six Lyoko Warriors realize they're up against two separate threats rather than one. Jeremie then helpfully says that since Tyron's latest update disrupted X.A.N.A.'s operations, he can likely use its lines of code to help design his virus against X.A.N.A..
- Yumi has a couple of firsts in this episode: This is the first time in season five which she pilots the Skidbladnir, also, this is the first episode in which she is virtualized twice in the same episode.
- First time Krabs and Tarantulas are seen inside the core of the Cortex.
- X.A.N.A. appears to be beginning to rebel against Professor Tyron, only using his supercomputer to gain full access to the network and nothing more.
- Professor Tyron speaks to Team Lyoko for the first time.
- Ninjas have a new special ability: they can fire a stream of bright green-colored energy and immobilise people, trying to trap them inside the Cortex by disconnecting them from Lyoko.
- Laura begins to learn about Franz Hopper, specially that he was the creator of the supercomputer and the virtual world of Lyoko, and how he suddenly vanished without a trace.
- This is the first time William is seen out of a scanner in Evolution.
- X.A.N.A.'s strength is shown to be at 80%, but as of the previous episode, X.A.N.A. had 85% control of the Web. Moreover, Odd is still carrying his Transwatch and says that he will "take care of the tower". So this episode should actually take place before The Codeless.
- When Ulrich's virtualization is running, it's seen that Odd is also in a process of virtualization, however, he is already on Lyoko.
- During William's virtualization, you see he is wearing a black leather jacket, and so is Yumi, while before in the scene where he was in the Supercomputer room, they are not wearing jackets. This is mostly because scenes are being reused.