Time Bomb
Professor Xavier warns the X-Men about an impeding event that wipes half the mutant population: Nitro will self-detonate in Genosha. The Brotherhood rescue Nitro from a government prison against his will and use Psylocke to control him, planning to use him as a weapon. The X-Men chase the Brotherhood in order to prevent Genosha's destruction.
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S1 E1
Hindsight (1)
A mysterious explosion destroys the X-Mansion right on the moment Wolverine was leaving. Professor X and Jean Grey are missing and perhaps gone for good causing the X-Men to disband. However, one year later, Anti-Mutant hunts Wolverine, and arrest a family that helped him, making him go after them with the help of Beast. Inside the jail, they free all the mutants, including Dust, Boom Boom and Pyro. In the end, Wolverine decides to find the others X-Men and fight the Anti-Mutants.
S1 E2
Hindsight (2)
Wolverine and Beast try to reunite the X-Men. They manage to get Iceman, Shadowcat and a resentful Rogue back to the team. Colossus, Angel and Cyclops say no. Meanwhile the Brotherhood of Mutants try to incriminate the X-Men and enlist Rogue as one of their members.
S1 E4
Overflow
Professor Xavier shows Wolverine a destruction of the African Continent. It's revealed Storm destroyed it. Meanwhile the Shadow King takes control over Storm's body and shows her the mainland burning, making her believe she needs to save it. Emma Frost ultimately beats the Shadow King.
S1 E6
X-Calibre
There is news that Nightcrawler was seen on a ship traveling to Genosha with other mutants, so the X-Men try to find him. Meanwhile, Nightcrawler and the other travelers (including Squidboy and Pixie) are intercepted by “pirates”, who really are Spiral and the Reavers, looking for fighters within the pool of high level mutants to take them to Mojo.