The third season of Code Lyoko originally aired from October 4, 2006 to October 23, 2006.
Story
Battle at the Core of Lyoko
X.A.N.A.'s monsters attacking the Core of Lyoko; the very essence of Lyoko itself.
A brand-new school year begins. Back from their relatively quiet two-week summer vacation, Lyoko Warriors quickly find themselves back at war with X.A.N.A.. The diabolical, rogue artificial intelligence who has made its way into the World Wide Web has raised the stakes with a new strategy of attack: wipe Lyoko off the digital map by destroying a huge transparent, white sphere, which located in a yet undiscovered chamber in Sector 5 directly below the arena of Carthage: the Core of Lyoko, and the Lyoko Warriors can't get in its way anymore. X.A.N.A. tries to destroy the Core in some episodes, and always fails at the last moment because the Lyoko Warriors prevent it. (Straight to Heart, Aelita, Temporary Insanity, Nobody in Particular)
Destruction of Lyoko's four Regions
X.A.N.A.'s own Code that allows him to gain full control to whatever he sees fit.
X.A.N.A. activates a tower in Forest Sector and launches an attack. When they go to Lyoko to deactivate the tower, suddenly, X.A.N.A. possesses Aelita through the Scyphozoa. Aelita enters the Forest Sector's way tower and destroys the sector with the Code X.A.N.A.; but luckily, it also deactivates the tower and X.A.N.A. is no longer able to control people. It repeats the same action in the Desert Sector, and Ulrich fails to prevent it. Later, X.A.N.A. possesses Michael Rouiler and damages the Supercomputer, doing a sabotage. It activates a tower in Ice Sector, but due to sabotage, Lyoko Warriors cannot reach the activated tower. Realizing the situation is desperate, Jeremie tells the Lyoko Warriors to hurry up. Aelita, seeing the activated Tower is too well-guarded, realizes they only have one choice: to destroy the Ice Sector voluntarily. Jeremie reluctantly agrees, and Aelita enters the passage Tower nearby and types in X.A.N.A., destroying the Ice Sector. Finally, the Mountain Sector is destroyed in the penultimate episode of the season by X.A.N.A. Aelita. (Lyoko Minus One, Tidal Wave, The Pretender, Sabotage, Double Trouble)
Adding William as the fifth Lyoko Warrior
William in the Factory about to be scanned.
In Lyoko Minus One and The Secret, William fights against his entire possessed class and a construction worker who is also under X.A.N.A.'s possession. In The Secret, William knows the secret and deactivates a bomb with seven seconds to spare. Later in the computer Lab, William is asking the team if he could join the group, Jeremie then proposes a vote, if anyone voted ‘No’ then William would not be accepted. The votes are counted and there is one no, William states that some people can’t help being jealous and leaves. Jeremie then launches a return in time. In Odd and Ulrich’s room, Odd, Ulrich, Jeremie and Aelita discuss the vote and Ulrich revealed that he voted 'Yes' to William stating that he would make a great Lyoko Warrior. Odd, Jeremie and Aelita then realizes that the person who voted no must have been Yumi. At the same time Yumi looks out her window and watches William roll by on his skateboard and says “Sorry William, but I don’t think you can be trusted”. But as fighting on Lyoko becomes harder and harder and X.A.N.A. Aelita has deletet the four external sectors of Lyoko, the group decides to let William join.
At the same time at Kadic, William tells Yumi that he had a dream about her. Surprisingly, he then goes on to quickly recount his involvement with the supercomputer in The Secret, which he should not have remembered after the return trip in that episode. William dismisses it as a silly dream because of the unbelievable nature of it. At the end of the episode, Yumi confirms that William's dream actually happened, much to his surprise. While they talk, Aelita wonders if he'll say yes. Odd insists that William would dive off of a cliff if Yumi asked him to. Jeremie asks Ulrich about the physics test, and for once Ulrich can say that he did well. Odd notes that their group is going though a lot of changes (adding William, Ulrich getting good grades), and the others agree. To symbolize William joining the group, he and Yumi shake hands. (Lyoko Minus One, The Secret, Double Trouble)
William's possession and the Annihilation of Lyoko
X.A.N.A. William destroys the Heart, thus putting an end to Lyoko itself.
In Final Round, the Lyoko Warriors are in the scanner room with William, who was accepted into the group. William swears he will not give away the secret. Soon William steps into the scanner to create a virtual image of himself so he can be immune to the Time Reversion program. Once that's done, the group warn William how dangerous X.A.N.A. is. Later, Aelita sees that X.A.N.A's attacking the chamber. She calls Jeremie, who is being interviewed by Milly and Tamiya and he cannot come. Odd is with Samantha Knight, who has returned in a skateboard championship. Ulrich is talking with his father. And Yumi is with Hiroki at home, but her little brother won't let her out of the house. Aelita contacts William, who is training in the forest. Excited about his first mission to Lyoko, he runs off to the Factory. Soon Aelita and William are virtualized on Sector 5. They go off to activate the key. Once in the room, they are encountered by Creepers. William joyfully goes to confront the Creepers while Aelita heads off to go and activate the key. William is destroying the monsters and Aelita is able to activate the key. But Aelita and William are then separated.
Suddenly the Scyphozoa arrives in front of William, but William ignores Aelita's inadvertence, and soon it catches him and possesses him. Aelita finally gets to William, but it's too late. A possessed William releases an energy wave at Aelita which devirtualizes her. The rest of Team Lyoko manage to reach the factory, but William went to attack the heart of Lyoko with Creepers and are ready to destroy it. Yumi, Odd, and Ulrich are virtualized on Sector 5, but William manages to devirtualize Odd and Ulrich quickly, and later devirtualizes Yumi, who tells William she knew it was a bad idea for him to join the group. William levitates to the heart, and then stabs it with his sword, which destroys Sector 5. Jeremie then says he wasn't able to rematerialize Franz Hopper, because he had found him on the Digital Sea. In Lyoko, William is floating in mid air, he opens his eyes and reveals his new form X.A.N.A. gave to him. In the Hermitage, the Lyoko warriors are thinking about how they will fight X.A.N.A now with Lyoko destroyed and what has happened to William. In Jeremie's laptop, a coding message appears in his screen, signed by none other than Franz Hopper himself, implying that he had somehow escaped the annihilation of Lyoko. Final Round)
Episodes
| Ep No. | Pro No. | Name | Image | French Title | Airdates |
| 1 (53) | 301 | Straight to Heart | 
|
Droit au cœur | US: October 4th, 2006 FR: September 9th, 2006 |
| 2 (54) | 302 | Lyoko Minus One | 
|
Lyokô moins un | US: October 5th, 2006 FR: September 16th, 2006 |
| 3 (55) | 303 | Tidal Wave | 
|
Raz de marée | US: October 6th, 2006 FR: September 23rd, 2006 |
| 4 (56) | 304 | False Lead | 
|
Fausse Piste | US: October 10th, 2006 FR: September 30th, 2006 |
| 5 (57) | 305 | Aelita | 
|
Aelita | US: October 11th, 2006 FR: October 7th, 2006 |
| 6 (58) | 306 | The Pretender | 
|
Le prétendant | US: October 12th, 2006 FR: October 14th, 2006 |
| 7 (59) | 307 | The Secret | 
|
Le secret | US: October 13th, 2006 FR: October 21st, 2006 |
| 8 (60) | 308 | Temporary Insanity | 
|
Tarentule au plafond | US: October 16th, 2006 FR: November 1st, 2006 |
| 9 (61) | 309 | Sabotage | 
|
Sabotage | US: October 17th, 2006 FR: November 2nd, 2006 |
| 10 (62) | 310 | Nobody in Particular | 
|
Désincarnation | US: October 18th, 2006 FR: November 3rd, 2006 |
| 11 (63) | 311 | Triple Trouble | 
|
Triple sot | US: October 19th, 2006 FR: November 6th, 2006 |
| 12 (64) | 312 | Double Trouble | 
|
Surmenage | US: October 20th, 2006 FR: November 7th, 2006 |
| 13 (65) | 313 | Final Round | 
|
Dernier round | US: October 23rd, 2006 FR: November 8th, 2006 |
Trivia
- Season 3 was the shortest season produced.
- Season 3 was the last season to have Sophie Decroisette as head writer. After this season, she was replaced by Bruno Regeste for Season 4, and then David Carayon for Season 5.