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As Jeremie and Aelita locate where X.A.N.A. might be, the group disembark in the re-programmed Skidbladnir through the Digital Sea, in hopes of destroying X.A.N.A. once and for all. As they arrive in the mysterious Replika, called the "Cortex", they find out that it is very much different from what they've experienced before.
Meanwhile, Odd is stuck at Kadic. William, who happened to be walking by, seizes the opportunity to help the group.
The heroes are waiting at the factory. To be more exact, they’re waiting impatiently. Odd is late, with the excuse that one of his classmates had managed to crack a new, unreleased game, not even commercially available. Jeremie scoffs the announcement and announces good news to the group: he and Aelita have reprogrammed the Skidbladnir. In a short while, the heroes will be able to return to the network and go to the supposed replika housing X.A.N.A..
Leaving via the tunnel in the park, the heroes come across William. He is indignant. He had completely understood that his “friends” were returning to the factory and he suspects something was wrong with X.A.N.A.
While William thought he had proven himself, Ulrich and Odd treated him very coldly, reminding him of his stupid behavior during his first mission on Lyoko and the fact that he was “captured like a rookie.” The group disperses but Yumi feels bad about the way the others have treated William.
Upon returning to Kadic, Odd goes to a secret meeting in the shadow of the cafeteria. He buys his hacked game for €20 (about $26 USD). However, while his contact disappears, Odd is trapped in the room by Jim, coming to close the door. He attempts to dial out, his phone isn't receiving any reception.
At the factory, having run out of patience, the others decide to go in without Odd. Yumi, Ulrich and Aelita travel to Sector Five. They find the Skid for the first time since its destruction by the Kolossus. They then go to the Digital Sea. Rapidly traversing the vast expanses of the network through a hub, they quickly arrive in view of the virtual world in while Jeremie had detected activity from X.A.N.A.. It is an unusual looking Replika; the outer shell is covered with growths of all kinds, as if it was bristling with spikes. Jeremie cracks the entry code without much trouble, and the heroes enter.
At the same time, Odd, still trapped in the cafeteria, is heard by William. Odd asks Dunbar to tell someone so he can be let out. William, still hurt by their exchange that morning, retorts ironically not to worry. He leaves, having understood that Odd’s concern is because the rest of the group is in the factory on a mission.
The Lyoko Warriors, exiting the Digital Sea, discover the new virtual world: the Cortex. It was no ordinary Replika; this world was composed of one unique sector. It didn’t correspond with anything they’d seen before. Immense floating platforms were organised around a large sphere resembling a nucleus. The visit commences. A serious and dark noise resonates throughout the sector. It then begins to move. The platforms diverge and come together, merge and separate.
Yumi crashes with her Overwing into a wall which had suddenly appeared in front of her. Her devirtualization is immediate. She does not appear back in the scanners. Jeremie realises that they need to get the codes to allow them to return Yumi to Earth. Ulrich and Aelita hurry on the Overbike in the direction of the core of the Cortex. On the way, the floor opens up just in front of the Overbike. The motorbike crashes against a wall, Ulrich falls to the floor and is devirtualised like Yumi; Aelita, all alone, is in flight thanks to her wings.
At the same time, at the factory, William arrives, in a mocking mood. Jeremy is upset to see him, but then decides to virtualise him into the Cortex to aid Aelita. William appears at the foot of the Skid. He takes a few seconds to admire the Cortex’s décor. When Jeremy offers to send him a vehicle, he responds that he has no need…and he rushes through the Cortex using Super Smoke…a “small memory of his X.A.N.A. period.”
At Kadic, Jim finally frees Odd from the cafeteria. When the teacher tells the boy that William never came to see him, Odd runs to the factory in rage, realising what William had done. Jim takes out his notebook and gives ten hours of detention to Della Robbia.
The situation returns to focus on Aelita. As well as the sector moving, Krabs had come to block her way. Nonetheless, the arrival of William made a massive effect. The ex-X.A.N.A. warrior destroys all the monsters in record time with superb martial art forms and sweeping blows with his sword and Super Smoke.
William and Aelita then approach the core, closed by a powerful door. Not even William’s sword can damage it…but after attempting, the door opens all by itself.
New Krabs appear. William sends Aelita into the core while he stays to take care of the Krabs. He’s then joined by Odd and the battle commences on several fronts. On one hand, Odd and William give the monsters a good beating, on the other, Odd wants so much to do it to William as well that the two almost end up fighting, not hesitating to make low blows.
In the core, Aelita uses teleporters that take her to a nebula-like room. She there discovers an interface and connects to find the rematerialisation codes for her friends. Dozens of images begin to flash before her eyes. These are images of the real world. While Aelita finds the codes, an image appears and stays on the screen; a photo of Franz Hopper, her late father.
The door of the core starts to close again and Aelita is conflicted to leave. On Earth, the codes work; Ulrich and Yumi reappear in the scanners.
Upon return to the real world, the heroes make a reluctant reconciliation with William, though they still do not fully accept him. Aelita asks herself why a photo of her father had appeared in the Cortex. Jeremy promises that he will try to find out what Franz Hopper has to do with the Cortex.
Afterwards, Jim is seen telling a group of students that if any of them are seen within 2 metres of the lunchroom door in the cafeteria, they will receive 10 hours of detention. Upon seeing and hearing all this from outside the cafeteria, Odd decides to get back at William. He tells William that Yumi was waiting for him inside the lunchroom and wanted to tell him something. William heads towards the lunchroom door, and is seen by Jim, who promptly gives him 10 hours of detention.
- This episode shares several similarities with the episode, Exploration.
- Exploring new territory.
- New territory shifts, eliminating a Warrior.
- Discoverers not automatically devirtualized.
- Most go to a terminal to get data on how to retrieve lost Warriors.
- Another Warrior is lost.
- Back-up sent.
- Data received; Warriors retrieved.
- The group finds a new territory: the Cortex.
- This episode marks the return of the virtual ship, Skidbladnir.
- This episode marks the debut of a new Replika, called the Cortex.
- The five Lyoko warriors reconcile with William, however it is unclear if he is officially part of the group.
- Aelita's Energy Fields are ineffective if they don't hit the Eye of X.A.N.A.
- It is shown that the Lyoko Warriors can be devirtualized if they fall from a high enough height or ram into something while on a vehicle going at maximum speed.
- The Portuguese subtitles can be found here: Cortex (episode): Portuguese Subtitles
- The Catalan subtitles can be found here: Cortex (episode): Catalan Subtitles