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Season 1 opens a year after Professor Xavier left with the Shi'ar. Cyclops leads the X-Men, Jean Grey is pregnant and the couple is thinking about leaving the team. Then comes the shock: Xavier left the school and the X-Men to Magneto. He tries to prove he's changed, stands trial at the UN and clashes with the group. Jean gives birth to Nathan, Storm loses her powers in an attack and a second Jean shows up. The one who gave birth is Madelyne Pryor, a clone made by Mister Sinister. The baby is infected with a techno-organic virus, and Madelyne and Cyclops hand Nathan to Bishop to be treated in the future.
The middle of the season changes everything. Magneto, Rogue and Gambit go to Genosha, the mutant nation. A giant Sentinel, Master Mold, attacks the island and kills thousands. Gambit dies destroying the machine. Storm gets her powers back in a duel with the Adversary, and Xavier returns to Earth. Behind the massacre is Bastion, a half-machine man who turns ordinary people into Prime Sentinels. Magneto answers with a magnetic pulse that shuts the machines down and kills thousands of humans. Later he rips the adamantium out of Wolverine.
At the end of S1, Jean taps into the Phoenix and takes down Bastion. Asteroid M falls toward Earth and the X-Men hold it back from inside and out, while Xavier goes into Magneto's mind to bring his friend back. Six months later, Bishop explains the X-Men aren't lost in space but in time: Cyclops and Jean in the far future with Mother Askani and Nathan, and Xavier, Magneto, Beast, Rogue and Nightcrawler in ancient Egypt, face to face with a young En Sabah Nur.
Season 2 is the war with Apocalypse. In the future, Nathan starts becoming Cable. In Egypt, the X-Men watch Apocalypse being born, and the pharaoh Rama-Tut turns out to be Kang. Most of them make it home, but Apocalypse kills Magneto in front of Xavier. In the present, Cable forms X-Force with Psylocke, Archangel, Jubilee and Sunspot, while Valerie Cooper runs X-Factor, a government team. Wolverine faces a Brood nest in a Weapon X facility, the Danger Room becomes self-aware and Nightcrawler ends up defending anti-mutant politician Graydon Creed, kidnapped by the Acolytes in the Savage Land.
Apocalypse brings Gambit back as his Horseman. In the finale, Cable shoots Gambit and frees Apocalypse's consciousness, which takes over the mutants. Rogue arrives with celestial power from Eson, saves everyone and traps Apocalypse in a crystal. Gambit lives, but Nightcrawler gave his own life to Eson. In the post-credits scene, Mystique kills Cooper and takes her place, and Creed becomes president.