List of X-Men: Evolution Episodes - Season Three

The remaining X-Men and Brotherhood members go to Area 51 to rescue their captive members. However, when Cyclops traps Mystique in Area 51 in order to blackmail her into giving up the location of where Charles Xavier is, the squads split. Without Professor X, the X-Men are now alone in a world that shuns them.

Despite rescuing Professor X, the bigotry towards mutants still exists as our heroes return to Bayville High, scorned and verbally abused by their human classmates, including their mutant-hating Principal Edward Kelly. Also, the School Board decides whether or not to allow mutants to attend school. However, Kelly enlists Duncan to team up with the Brotherhood (Avalanche, Toad, & Blob) to ensure a permanent mutant ban.

Wanda wants to find out where her father Magneto is, so she enlists Caliban for help. She then goes to her brother Quicksilver for info. When he refuses, Wanda delivers him to the police. When the Brotherhood tries to break him out of a prison transport (as part of Magneto's offer from Gambit), Rogue and Shadowcat appear to break up their rescue operation.

Jean is about to confess her strong and deep mutual romantic love to Scott when Mystique (who managed to escape from Area 51 and is out for revenge) abducts Scott and abandons him in the desert in Mexico without his ruby quartz glasses. Jean, who has vivid telepathic visions of him in peril, tracks him down, but Mystique is determined to kill them both.

Spyke joins a skateboarding contest sponsored by "Pow-R 8" soda. However, Pow-R 8 is harmful to mutants, and when Spyke drinks a swig, his mutation greatly advances, poisons, and disfigures him seriously. He is saved by the Morlocks, and in the end, Spyke joins them.

Wanda tracks down Magneto to his Acolyte headquarters in a nearby ski resort. Meanwhile, Kurt is spending time with Amanda Sefton and meeting her parents. In a bid to win Wanda's affections, Toad steals Nightcrawler's image inducer (thereby blowing his cover in front of the Sefton household) and pursues Wanda, followed by an angry Kurt. However, when Wanda gets abducted by Magneto and is brainwashed by Mastermind into believing her father was a kind and giving man (erasing her memory of the asylum she was sent to), the two team up to rescue her.

Angel spots Gambit stealing a mysterious artifact, but when he tries to stop him, Mesmero fights him off. When the Acolytes want to steal another artifact, the X-Men fight them and discover there is a bigger plan happening. Soon both teams will face a spider-like being which is virtually unstoppable.

Taking a break from superhero duty, the X-Men (without Rogue and Berzerker) take a pleasure cruise. However, Magma becomes violently ill, literally suffering from earth withdrawal. When Boom Boom and Iceman take her to an island, she accidentally triggers a volcano. When the volcano threatens to explode again, Magma dives into its heart to silence it once and for all.

A mysterious female assassin terrorizes the X-Mansion, knocking out the X-Men one by one. Wolverine finds out that it is his clone, created by the Dr. Deborah Risman and raised without love by HYDRA, and she wants to kill him because she holds him responsible for her miserable life. Wolverine and X-23, as she is called, square off in a battle that Wolverine does not want to win.

Rogue falls under the mind control of Mesmero and is used as a weapon to absorb the mutant abilities of every X-Man, Brotherhood, and Acolyte member. The three factions reluctantly cooperate and find out that Mesmero wants Rogue to give all of her stolen abilities to Apocalypse to awaken him.

The X-Men, Brotherhood, and Acolytes track Apocalypse to Egypt, but fail to prevent him from coming back to life. Mankind is now in terrible danger.