A young teenager has been rejecting her mutant powers ever since she discovered them. But when giant robots track her down, it's up to the X-Men to save her.

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.

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.

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.

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.

The X-Men are divided and conquered, by none other than a friend they had thought dead.

The X-Men barely survive their return trip from space, Jean Grey discovering herself changed by the experience. Professor Xavier's dark half is given form, and proceeds to attack his students.

Lilandra seeks to protect the M'Kraan Crystal from her wicked brother, the Emperor D'Ken. But the interstellar pirates known as the Starjammers capture it, and Cyclops, in an effort to enact their own revenge scheme on the emperor.

Shi'ar Emperor D'Ken's rise to power via the M'Kraan Crystal is causing a universal implosion. The X-Men, Imperial Guard, and Starjammers find themselves overpowered and unable to stop it. Jean Grey must unleash her destiny as the host of the Phoenix, even at a most personal cost.