Cyclops and Iceman are still working to stop the Mutant-Master from launching the missiles. Cyclops has a plan to mess up the base’s air filtration system so Factor Three cannot use their knockout gas to take over the base. But they soon encounter Mastermind and Unus.
Meanwhile, Marvel Girl and Beast work together to obtain keys to their cell from a guard. Marvel Girl, Beast and Angel quickly escape and attempt to obtain the briefcase containing the “time-bomb”. But the Blob catches up to them, knocks Beast out and grabs the briefcase from Marvel Girl’s telekinetic grasp.
Cyclops and Iceman are ambushed by the military base’s guards as well. They create an ice fog to cover their escape.
Marvel Girl, Beast and Angel corner Blob to get him to surrender the briefcase. Marvel Girl plants the idea in Blob’s head that the Mutant-Master is angry at Blob for getting captured and possibly foiling his plans that he intended to blow Blob up along with the X-Men. That is enough to get Blob to hand over the briefcase. Angel grabs it and flings it high into the sky, exploding overhead. The castle guards see that the X-Men have saved their lives and release them.
Cyclops discovers a homing signal on the “flying egg” enabling him and Iceman to find the Mutant-Master’s new lair. They sneak in but are found out by the Vanisher, Unus and Mastermind. Just then, Marvel Girl, Angel and Beast appear. The whole team is reunited.
Suddenly, Xavier appears, having escaped his confinement. He reasons with the evil mutants that the real enemy is the Mutant-Master, and that they should join forces with the X-Men to stop him. Angry that he has lost control of the evil mutants after Xavier exposes his plot to destroy Earth, the Mutant-Master commands his androids to take out all the mutants.
Banshee regains consciousness and with his powers, shatters the platform of the Mutant-Master, revealing his true, alien form. The X-Men and evil mutants work together to defeat the Mutant-Master. Ashamed of his failure to conquer a planet, the Mutant-Master commits suicide.
While the evil mutants do not agree to become the X-Men’s allies, they do agree that the Mutant-Master’s lair must be destroyed. Xavier is hopeful that fighting against a “common foe” may be one step closer to uniting good and evil mutants.
Upon returning to the mansion, Marvel Girl surprises her team mates with new, personalised costumes that she had been working on in secret with Xavier. Xavier acknowledges that the X-Men are not “children” anymore and deserve to look like individuals.
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