Plot 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. The 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 progressed, the real Xavier is found, Mystique is defeated, the mansion 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 forge a deeper relationship, and Spyke leaves the X-Men when his power 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 seasons final episodes. Mesmero manipulates Magneto into opening the second door, and uses Mystique and Rogue (Rogue being hypnotized) 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.