Season Three

Season Three of X-Men: Evolution premiered with Day of Recovery on September 14, 2002, and began its episodic run til August 16, 2003 ending with the two part finale episode of Dark Horizon. It was succeeded by Season Four, which debuted on August 30th of the same year.

Summary
In Seasons Three and Four, the show notably begins to take a much more serious tone. After the battle with the Sentinel, the mutants are no longer a secret and public reaction is one of hostility. The show is brought into more traditional X-Men lore, dealing with themes of prejudice, public misconception, and larger threats. As the season progresses, the real Xavier is found, Mystique is defeated, the mansion is rebuilt and the X-Men allowed back into Bayville High. Wanda continues to search for Magneto (who was saved by his son, Quicksilver, at the last minute) until Magneto uses the telepathic mutant Mastermind to change her childhood memories. Scott and Jean develop a stronger and closer romantic relationship (particularly after Mystique kidnaps Scott and brings him to Mexico), and Spyke leaves the X-Men when his mutant ability becomes uncontrollable, deciding to live with the sewer-dwelling mutants, the Morlocks.

As part of the series arc, Rogue loses control of her powers, leading to her hospitalization. During this time, she learns she was the adoptive daughter of Mystique. Mystique, through the visions of the mutant Destiny, foresaw that the fate of Rogue and herself lay in the hands of an ancient mutant that would be resurrected. Apocalypse emerges in the season's final episodes. Mesmero manipulates Magneto into opening the second door, and uses Mystique and a hypnotized Rogue to open the last, turning Mystique to stone in the process. Now released, Apocalypse easily defeats the combined strength of the X-Men, Magneto, the Acolytes, and the Brotherhood before escaping.