Breaking into the Mutant Control Agency's headquarters to destroy the registration files on mutants, the X-Men lose two of their members against the Sentinels, but eventually gain another.

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.

Wolverine must overcome his feelings for Jean, and Storm must overcome her crippling claustrophobia, when the team journeys into the sewer to rescue Jean Grey & Cyclops from a race of hideously deformed mutants known as Morlocks, and their leader Callisto, who wants to make Scott her king.

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.

Gambit, Storm, and Jubilee become slave labor on the island resort of Genosha, along with other mutants, forced to help build the new power source for a Sentinel factory. They're given aide in escaping by a mysterious mercenary named Cable.

The X-Men return from Genosha, finding the home destroyed, and Professor Xavier missing. They suspect a super-strong Russian mutant named Colossus, but the real culprit turns out to be someone more human, far tougher, and with deeper ties to the Professor.

Rogue seeks a scientist who claims to be able to "cure" any mutant of their powers, unaware that neither he, nor his process, are what they appear to be.

An ancient and immensely powerful mutant, known as Apocalypse, creates four Horsemen to help usher in a new world where survival of the fittest reigns.

A mutant from more than half a century into the future, named Bishop, arrives in the present, attempting to change history for the better, by stopping an X-Man from committing an assassination. But between being chased by a future breed of Sentinel, and the details of his mission being fuzzy, he's got his work cut out for him.

Aware of an impending assassination which will create a catastrophic future, the X-Men must deal with threats both outside and within their team.

Prominent anti-mutant and presidential hopeful Senator Kelly is caught in a tug-of-war between Magneto's goal of mutant superiority, the X-Men's dream of peaceful co-existance between mutants and humans, and the mutant-hunting Sentinel robots' goals of global domination.