PLOT
Season one
The first season introduces the core characters and lays the foundations for future story lines. Professor X, Cyclops, Wolverine, Storm and Jean Grey make up the original X-Men. As the season develops, the ranks of the X-Men are bolstered by the appearance of Nightcrawler in the first episode, Shadowcat in the second, Spyke in the fifth and Rogue (who originally joins the Brotherhood in the third episode) in the seventh. In the later episodes of this season, Nightcrawler discovers the identity of his birth mother, Wolverine finds answers to his past, Rogue switches sides to join the X-Men, and Xavier's half-brother, Juggernaut, is released from his prison.
Confrontations are typically with the Brotherhood, who vie for new recruits with the X-Men over the course of the season. Toad is the first to be introduced, followed by Avalanche, Blob and Quicksilver. The Brotherhood, led by Mystique, are in fact being directed by a higher power, the identity of whom was "revealed" in the two-part season finale as being Magneto. After Cyclops discovers that his brother, Alex, actually survived the plane crash that killed their parents, they are both taken by Magneto into his "sanctuary" on Asteroid M. Magneto captures several X-Men and Brotherhood members in an attempt to amplify their mutant abilities and remove their emotions. Asteroid M is destroyed by Scott and Alex Summers, but not before two unidentified metal objects fly from the exploding rock.
Season two
The second season sees the addition of several new mutants, including Beast, who becomes a teacher at the Xavier Institute and an X-Man, as well as a version of the New Mutants: Boom Boom, Sunspot, Iceman, Wolfsbane, Magma, Multiple, Jubilee, Berzerker, and Cannonball. During the course of the season, it is revealed that the villains who supposedly perished on Asteroid M are in fact alive. Sabretooth continues his pursuit of Wolverine, while Magneto continues to work his own agenda.
Mystique poses as Risty Wilde, a high school student at Bayville High who befriends Rogue and breaks into the mansion to steal Xavier's Cerebro files. Using the files, she recovers Wanda Maximoff, the Scarlet Witch, Magneto's daughter and Quicksilver's sister. The mentally unstable mutant joins the Brotherhood upon Mystique's return, allowing them to defeat the X-Men in a battle at the Bayville mall. Before the finale, a pivotal episode aired featuring the telepath Mesmero opening one of three doors that would unleash a mutant known as Apocalypse.
I n the season finale, Xavier rigorously trains his X-Men to face Magneto, pairing them with the Brotherhood. Cyclops, furious with having to work with his former adversaries, leaves the team. The mansion is later set to self-destruct with Cyclops and several students still inside. Magneto, meanwhile, recruits Sabretooth, Gambit, Pyro, and Colossus as his Acolytes to fight the X-Men/Brotherhood team.
At the same time, Wolverine is captured by Bolivar Trask to use as a test subject for the anti-mutant weapon, the Sentinel. Magneto continues to manipulate events by unleashing the Sentinel onto the city, forcing the X-Men to use their powers in public. Wanda tracks down Magneto and attacks him while he is trying to deal with the Sentinel that is targeting him. The Sentinel is damaged and apparently crushes Magneto as it falls.
When the mutants who have not been captured by the Sentinel return to the remains of the mansion, Cyclops and the students emerge from the explosion unharmed. Scott throws Xavier from his wheelchair and blames him for blowing up the mansion. Everyone is shocked as Xavier calmly stands up, transforming into Mystique.
Season three
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 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 season's 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.
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