As the Beast faces an arraignment in court before a mutant-hating public, the X-Men unwillingly take in an old enemy of Wolverine's. Magneto, an old friend turned enemy of Professor Xavier's, attacks a military base in an attempt to unite mutants against humanity.

Magneto & Professor Xavier come face to face for the first time in years amid an exploding factory, while Sabretooth & Wolverine face off in the mansion.

Having left the X-Men to seek peace in the arctic, Wolverine instead finds himself battling Sabretooth for the safety of an Inuit tribe. Storm, Gambit, and Jubilee investigate an island resort which welcomes mutants, and might be too good to be true.

Wolverine is led back to his homeland of Canada, and is attacked by his former teammates from the supergroup Alpha Flight. The government wants the secrets of his adamantium skeleton back, and are willing to take him apart to get it.

A cryptic postcard unleashes a flood of maddening and painful memories in Wolverine that threaten to drive him insane. To keep his mind from being torn apart, Wolverine and Beast travel to the one location that may hold the answers to his hidden past: the ruins of the top-secret Weapon X lab where Wolverine's bones were laced with adamantium. There he encounters other former 'test subjects'—Sabretooth, Maverick and Silver Fox—who are suffering similar mental breakdowns.

When Oracle, the psychic member of the Imperial Guard is kidnapped by Apocalypse, Professor Xavier deduces his scheme involves capturing mutants with telepathic abilities. The X-Men are split up to track them down before the villains can, which puts Wolverine & Shard in the middle of a scuffle between Archangel and a ninja named Psylocke.

Rushing to investigate a disturbance downtown, the X-Men find Sabretooth on the rampage again, but realize too late that it isn't really Sabretooth at all. It is the Phalanx, a voracious alien life-form that can assume the guise of anything or anyone. Before long, the X-Men are all captured, except for Beast, who must find a way to stop the alien horror from devouring the entire Earth.