Cyclops, Marvel Girl and Beast use mini-Cerebro to track down the whereabouts of Angel, Iceman, Lorna and Havok. They are led to the countryside, and mini-Cerebro indicates that they are held deep underground. But they fly into a trap and their jet is shot down from the sky. Marvel Girl uses her telekinetic powers to slow their descent, as instructed by Cyclops.
Larry watches the X-Men’s jet explode and thinks that he has killed the rest of the X-Men. But the Sentinel refuses to release Larry from its grasp. Chalmers retells Larry’s forgotten past. Larry has the powers of premonition and had predicted the exact nature of his mother’s death. His father created the medallion to suppress Larry’s powers and his memory. As well as the Sentinel program to protect Larry from finding out the truth. The Sentinel puts Larry into a containment pod. Chalmers is unable to do anything because the Sentinels are not programmed to obey him.
Outside, the Sentinels have captured Quicksilver, Scarlet Witch, and the Toad. As well as Unus and Mastermind. They also detect Magneto and set off to find him.
Meanwhile, Cyclops, Marvel Girl and Beast scale the cliff, hoping to find a way inside. They enter through a fissure but a Sentinel spots them. Together, they are able to take down one Sentinel. More Sentinels arrive with the capture of more mutants. Seeing the chance to get to the centre of the lair quickly, the X-Men hop onboard the “cargo” of mutants.
Cyclops, Marvel Girl and Beast trade places and costumes with Quicksilver, Scarlet Witch and Toad. The Brotherhood are freed and told to keep out of the X-Men’s business. The Sentinel who captured the Brotherhood realises that the mutants it captured have changed. Beast knocks the Sentinel out with the “weighted boots” designed to keep Toad from escaping, aided by Cyclops’ optic blast. The X-Men hurry inside as more Sentinels attack them.
The other Sentinels are unaware that Cyclops, Marvel Girl and Beast are in disguise. These Sentinels have “adapted” themselves to attack Scarlet Witch, and are caught offguard by Marvel Girl’s telekinesis. Beast keeps the other Sentinels busy. Cyclops charges into the central control room.
Chalmers sees Larry staring at gun on a table, and imagines that Larry wants him to murder Havok. Cyclops enters to see Chalmers fire the gun at Havok’s head. A Sentinel detects Cyclops and blasts at him. Chalmers jumps in front of Cyclops and is blasted instead. This incident activates an emergency protocol in the Sentinel’s system as they are programmed to never harm humans. Cyclops sees the opportunity to destroy the control panels and release the mutants.
Havok blasts a Sentinel approaching Cyclops from behind. The rest of the Sentinels however are more preoccupied with tending to Chalmers. Chalmers tells Cyclops to use the Sentinels’ “logic” against them. Havok feels his powers building up inside of him.
Cyclops poses a question to the Sentinels: If mutants are descended from humans, that makes mutants humans, and the Sentinels have to protect humans from becoming mutants. The Sentinels deduce that the “source” of mutation is the sun and collectively fly towards it, destroying themselves in the process.
Havok is unable to control his powers. He runs into the control panel and explodes his powers. After the Sentinels leave, Cyclops rushes to his brother’s side but finds him unconscious. Knowing that Havok needs a doctor, Cyclops contacts a former colleague of Xavier’s, Dr Lykos.