Cyclops, Beast and Marvel Girl are using a mini Cerebro unit to track down all of the mutants that have recently been captured by Larry Trask's Sentinels. However, their jet-car is blasted out of the sky causing the three X-Men to fall to their doom, but they are rescued at the last minute by Jean's telekinetic powers.

While in the secret hideout of the Sentinels, it has been revealed that Larry Trask, ironically, is a mutant himself, a revelation that is learned when the medallion given to him from his father was accidentally removed and turns out to have nullified and shielded his mutant powers from the Sentinels scanners. This is confirmed by Judge Chalmers who knew the truth all along and explains that Larry's father the late Bolivar Trask created the medallion after Larry's mutation precognition powers foretold his mother’s death. With the Sentinels no longer following his orders now that he has been outed as a mutant, the Sentinels carry out Larry's last command as a "human", to capture all the remaining mutants and destroy them.

In rapid succession, the Sentinels seek out and attempt to capture the remaining mutants left in the world. They find opposition when trying to capture Quicksilver, Scarlet Witch and Toad; however easily manage to capture Mastermind, Blob and Unus. While Judge Chalmers begins to consider what to do about this situation, not wishing to be party to the genocide of all known mutants, the Sentinels detect a concentration of mutant energy signatures. This turns out to be Cyclops, Marvel Girl and the Beast who are now scaling the mountain which hides the Sentinel base. They are opposed by Sentinels which they easily defeat and manage to break into the Sentinel base.

Inside, they hide as a Sentinel prisoner craft arrives with the captured Quicksilver, Scarlet Witch and Toad. Realizing that the Sentinels are conditioned to deal with any given mutants threats by identifying who they are, the three X-Men trade costumes with the former Brotherhood of Evil Mutants members, Cyclops taking Quicksilver's costume, Marvel Girl taking Scarlet Witch's and the Beast wearing Toad's. When the Sentinels that captured the three other mutants attempt to take them to the holding chambers they are caught off guard. Confused by the unique costumes and not prepared to deal with different powers, the Sentinels fall easily to Cyclops, Marvel Girl, and Beast's counter attack on the Sentinels.

As this is happening, Judge Chalmers awakens Larry Trask from his suspended animation. Larry has a vision of Havok getting injured in the coming battle. When Chalmers asks what he can do to stop the Sentinels, he traces Larry's glance at the device he used to neutralize Havok's powers earlier, however Chalmers misinterprets Larry's attempts to tell him what the gun is for as an order to kill Havok, which Chalmers refuses to do.

Cyclops and the others fight their way into the main chamber just as the Judge realizes what the gun is really for and uses it to reactivate Havok's powers. Realizing what Chalmers has done, the Sentinel in the room blasts him before Cyclops can attempt to destroy it. Cyclops then blasts open the cyro-tube that is keeping Alex in suspended animation. Now free, Havok turns his powerful cosmic energy blasts on the Sentinel.

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