In the Savage Land, Mr. Sinister shows his "guests" (Professor Xavier, Jean Grey, Magneto, and Morph) to their room, a steel-doored cell in the dungeon. He promises them that they, and the X-Men, will live on through their culled genes when he soon creates his army of Super Mutant slaves. Magneto warns him that he's underestimated the team, and Xavier is distraught over having lead his students into a trap.
Soon, the Blackbird touches down upon the crest overlooking the Savage Land. Beast is awed by the uncharted jungle valley hidden within Antarctica. The X-Men find the wreckage of Xavier's mini-jet, and when Rogue tries to lift up a large piece of metal to search for clues to the Professor's whereabouts, she discovers her powers are gone! One by one, each of the X-Men finds themselves powerless (Beast isn't changed, since his "powers" are superficial, and Cyclops is able to take off his visor without unleashing laserblasts). Before they can question the loss, the combined forces of the Nasty Boys, Mutates, and the Skyriders arrive. The X-Men, without the aid of their powers, hold their own well for a moment or so, but eventually are captured. All, that is, except for Wolverine, whose ability to unsheathe his claws is unaffected by the lack of a mutant healing factor (though it still hurts him). He works his way through the villains, and when Vertigo attempts to bring him to his knees, he leaps off the side of the cliff, landing safely in the river below.
While the X-Men are led in chains to the citadel, Wolverine races through the wilderness, dodging attacks from the Skyriders. Even once he loses them, he runs afoul of a small dinosaur. It's only sheer luck that said dino ends up chased off by another, a bigger tyrannosaurus rex, that Wolverine is able to escape unharmed. He cuts his way through the jungle, and when he discovers Ka-Zar and Zabu tracking him, he gets the jump on the native pair before they can him. Ka-Zar believes Logan to be one of the Mutates, and the misunderstanding leads to a brief brawl between the three. Wolverine's claims of being on his same side lead to their joining forces, in an effort to free the other Savage Landers from the great citadel. The Skyriders once again attack, but this time, Ka-Zar is able to snag a saddled-pterodactyl for his and Logan's use in getting to their destination quicker (Zabu has to stay behind).
At the citadel, Mister Sinister is goaded into elaborating on his grand schemes: taking mutant-kind to the next level. He scoffs at Xavier's desires of coexistence with humans, and at Magneto's rallying for war against non-mutants, noting neither can win at their goals. The eventual outcome Sinister wants is an ultimate race of mutants, each member containing the combined powers of all other mutants. As a test run of his machine to do this combining of DNA, Sinister has Magneto's powers transferred to Vertigo. It proves to be a success, causing her normal one-person dizzying powers to be amped to massive, unweakening waves, which overwhelm all of the imprisoned X-Men. Rogue, confiding in Gambit that she's scared, unaware of how to fight them without her powers, is chosen to be next in the process. Gambit urges her to be brave, telling her something he's never told any woman before, that he loves her, and they exchange a brief kiss before she's taken away.
Meanwhile, Ka-Zar and Wolverine land atop the roof, and once inside, split up to rescue their respective friends. Wolverine tears into the Nasty Boys and Mutates, but once again Vertigo proves to be most challenging. Ka-Zar knocks out a guard, thanks to his wife Shanna distracting him, and frees his fellow villagers. Together, they all storm Sinister's lab, providing only a brief diversion, but enough for Wolverine to free Morph and Xavier from their binds before passing out. Vertigo tries to disorient them, and pushing through the pain, the pair of mutants manage to damage enough of Sinister's machines to deactivate the signal which is depowering everyone without a belt. The X-Men free themselves with their restored powers, and together rumble against the Nasty Boys and the Mutates, Magneto getting revenge on Vertigo by sealing her unconscious with metal, and the recovered Wolverine finally shutting Ruckus up. Cyclops, the only one who can harm Mr. Sinister, begins blasting the evil geneticist, demanding once more that he leave him and his friends alone. Sinister reactivates the implant on Morph's brain, turning him evil long enough for him to get out a lasergun and fire upon Xavier. He prepares to do the same to Cyclops and Jean, who are locked in an evenly-matched tug-of-war with blast-beams, when the Professor reaches into his mind, and reminds him that he's one of the X-Men, and is part of their family. Overcoming the control once more, Morph instead fires upon Sinister, who is blown to pieces. With their leader shattered, the Nasty Boys and Mutates scatter, though Brainchild tries to piece his master together again. Noticing the chunks of Sinister starting to re-form, Jean uses her telekinesis to fling them all into the air, assuring that it will take him a while to become whole once more.
Suddenly, thanks to Sauron's activation of the self-destruction sequence, the citadel begins to explode around them! Magneto creates a forcefield, and is able to protect himself, the X-Men, and the Savage Landers. Soon, the X-Men are helping to repair some of the damaged huts within the village. Xavier, back in his hoverchair, is pleased that his students were able to continue his work without his being around for them. He plans to remove Sinister's brainwashing device from Morph when they return home, but the emotional damage from what he went through will take much longer to repair. Magneto found it good to fight on Xavier's side again, but when offered to join him permanently, he declines, noting they both have their own destiny, and only the future will prove which one is right. Xavier bids goodbye to his old friend, and the X-Men exit the valley in the Blackbird, right behind Magneto.
With the final "outlanders" out of the way, Sauron prepares to guide the Savage Land to its true future. And speaking of the self-proclaimed herald of the future, on the shore of the river, the grains of sand form into the shape of Mister Sinister's smiling face, laughing wickedly with eyes gleaming red...