Riots break out in the streets after the kidnapping of Senator Kelly. Mutants in general are blamed for the kidnap. Xavier urges the X-Men to find and rescue Kelly before the anti-mutant violence escalates, even if Kelly isn’t exactly their ally.
Magneto is revealed to be Kelly’s kidnapper. He has learned that the death of Kelly will ignite the wave of human-mutant conflict. With his motive to destroy humans and put mutants in power, Magneto is poised to kill Kelly himself when he is interrupted by Sentinels. The Sentinels ultimately take Kelly from Magneto.
The X-Men arrive at Magneto’s hideout too late as Magneto is found unconscious and Kelly is kidnapped yet again by the Sentinels.
Trask had the Sentinels bring Kelly to an abandoned mine and the hideout of Mastermold. Mastermold has the intention of turning humans into Sentinels, with Kelly as the first victim of the experiment.
Xavier probes Gambit’s mind to gather information about the Sentinels who have gone into hiding. Gambit’s last encounter with them was on Genosha. A name, Gyrich, pops up.
The X-Men track Gyrich, and Wolverine threatens answers out of Gyrich. They are told of the abandoned mine hideout. Having just been informed by his partner Trask that the Sentinels have turned on them, Gyrich hopes that the X-Men and Sentinels might do themselves in in trying to destroy each other.
Xavier plans an attack and rescue mission. The team is split in two. Cyclops, Jean, Gambit and Wolverine are to enter the mine, seek out Kelly and rescue him. Storm, Rogue and Jubilee, with Xavier, are to remain above ground and back up their team mates when the Sentinels attack.
The rescue team find Kelly with Mastermold. Jean uses her telekinesis to get Kelly out of the room, but the rescue is spotted by Mastermold. They begin assaulting the Sentinels. The room explodes and the X-Men make haste to the surface with Kelly as more Sentinels give chase.
The X-Men surface with Kelly, and so does Mastermold. Xavier, piloting the Blackbird, instructs Cyclops to blast at Mastermold’s head. Flying the Blackbird into Mastermold and cutting its head off, Xavier succeeds in taking out Mastermold. He parachutes to safety, with the assistance of Rogue.
After the X-Men have come to his rescue, Kelly has a change of heart about mutants. He now strives towards Xavier's goal of human-mutant co-existence as he runs for President. Beast is released from prison. After recent events, Scott and Jean decide to tie the knot. Eerily, the couple is being watched by a mutant known as Sinister.
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