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.

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.

As the Dark Phoenix grows increasingly hostile, even destroying an entire star system, the X-Men struggle to figure out a way to stop her without harming their teammate Jean Grey.

The X-Men face the Shi'ar Imperial Guard in a trial by combat to spare the life of Jean Grey, though even they begin to question the safety of the universe as long as the Dark Phoenix remains alive inside her.

At a Mutant/Human Relations Summit, Henry Peter Gyrich attacks.

Gambit, Rogue, and Wolverine take a ski trip in Germany. While Gambit and Rogue seem to be enjoying themselves, Wolverine is restless, and longs for some action. When he hears reports of a demon hiding in a local monastery, his investigation reveals not a demon, but a mutant, Nightcrawler, whose devilish appearance is in stark contrast to his peaceful and deeply philosophical nature.

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.

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.

Professor Xavier's claims of the capture of his alien soulmate Lilandra by Juggernaut and Black Tom Cassidy are met with skepticism.

The Circle Club makes the Phoenix-controlled Jean Grey their new Queen, but finds two factors opposing it: her mental bond with Cyclops, and the presumed-dead Wolverine stalking after them.

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.

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.

Following visions from recent dreams, Professor Xavier sends his X-Men on a mission to the Eagle One Space-Station, putting them in the middle of an interstellar conflict.

Fueled on by his desire to seek vengeance against the immortal mutant that changed him into a weapon of evil, Archangel persaudes Rogue into helping him hunt down and destroy Apocalypse.

Nightcrawler gets a mysterious message. He is informed that his birth mother (whom he never knew) is in trouble. He turns to the X-Men for assistance. Jubilee is baffled that Nightcrawler wants to help the mother who abandoned him -- she has never known her birth parents and feels pretty hostile toward them, whoever they are. Nightcrawler admits there has been pain, but his faith in God has helped him overcome her rejection. The plot thickens when one of the team members recognizes Nightcrawler's mother's voice.

Wolverine thinks back to the time when he fought during World War II and teamed up with Captain America.

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.

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.

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.

The flirtation between Cyclops and a mutant singer named Dazzler exacerbates the Phoenix-controlled side of Jean Grey, leaving her open for manipulation by a secret sect of mutants coveting her immense powers for their own evil designs.

A founding member of the X-Men, named Iceman, breaks into a government facility. He refuses to trust his former teammates about his reasons for doing so, but when Jubilee aids him in his quest, it leads to the team going up against another group of mutants, known as X-Factor.

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.