Weary of battling for mutant supremacy, Magneto offers to transport all mutants to an orbiting asteroid named Asteroid M where they can live peaceful and human-free lives; however, Fabian Cortez tricks Magneto into an escape pod and launches him into space. When the X-Men arrive to investigate Magneto's intentions, Cortez blames Magneto's disappearance on them and accuses them of assassinating Magneto. When the X-Men try to escape, Gambit sacrifices himself and the other X-Men escape.
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As Magneto plummets helplessly to Earth, Fabian Cortez assumes control of Asteroid M and sends hundreds of missiles towards Earth. Meanwhile, Rogue goes to help the X-Men and tries to find a missing Gambit. Magneto frees himself and returns in time to destroy both the missiles and Asteroid M. Everyone escapes before the asteroid is destroyed and they all return home (Gambit included!) Meanwhile, Cortez is rescued from the descending asteroid by Deathbird...and Apocalypse.
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. Later they find out that many of their memories were implanted, and their true memories are destroyed with the lab.
When Cyclops flies solo to a tiny, western, desert community to see an old friend, his plane is blasted out of the sky. Injured and unable to use his powers, he struggles into town, only to discover his friend is missing and the town is caught in the grips of a militant, mutant-only, anti-human hate group: the Children of the Shadow. The Children of the Shadow hunt him down. When his powers return, Cyclops gets help from some mutants and defeats them.
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. Later the townsfolk attack and burn the monastery. The X-Men convince the townsfolk not to fear what they do not understand, and Wolverine too learns something about the nature of faith.
The day Morph rejoins the X-Men, terrorists attack a top-secret, high-tech weapons factory; the alert interrupting his homecoming party. Morph and Wolverine investigate and discover that the Sentinels are back. Morph hesitates to fight the Sentinels and has a flashback of getting shot by one of them. Eventually he overcomes his fear and defeats them, but he leaves the X-Men in the end saying he's not ready yet.
When Proteus discovers that his "deadbeat dad" is a prominent politician, he storms the Union Hall right in the middle of his dad's campaign speech on 'family values.' Proteus tells his father that he is his son but his father denies it and runs off in horror, crying for help. Angered at his father's reaction, Proteus creates havoc, but Professor X later calms him down and he stops the rampage. He then goes back to Muir Island with Moira MacTaggert.
Trevor Fitzroy and Bantam travel back in time to 1959 and kill Professor X as Master Mold ordered them. This creates an alternate present time-line, where a human-mutant war has destroyed everything. Bishop and Shard arrive in 'alternate present,' where humans battle violently against 'The Leader' Magneto, and his followers who include husband and wife Wolverine and Storm. Bishop and Shard recruit Wolverine and Storm to help stop Fitzroy, but they fail.
Failing to stop the assassination of Xavier, Bishop, Shard, Storm, and Wolverine travel forward to the future, a future changed so much that Forge's time travel machine has never been tested, and Forge has no idea who these four time travelers are. After they convince Forge, they go back a few minutes before Xavier died and save him. Everything reverts to normal.
In 3999, Apocalypse tricks Cable and steals Cable's time device to travel back in time, but he accidentally falls into the Axis of Time. Apocalypse hires Mister Sinister to kidnap psychics all across the universe. Meanwhile, Jean and Scott try to get married again.
Cable uses another time-machine and comes to the present to get the X-Men's help in destroying Apocalypse's Lazarus Chamber. They go back in time to ancient Cairo and destroy the Chamber. Apocalypse plans to use the psychics to destroy all time, and recreate a universe where he will rule unchallenged.
As the true and terrifying nature of Apocalypse's final plan emerges, several in his band team up with the X-Men to stop him. With Bishop's help the psychics are freed. At the end the psychics move Apocalypse to the Astral Plane, so he could age without the help of his chamber.
In a New Mexico desert, Wolverine witnesses the crash of a spaceship carrying horrific, alien bug-like creatures -- the Family -- which overwhelm him. Rogue reunites with her first boyfriend, Cody, who ends up being a part of the Family's plot to have Rogue become their new leader. The X-Men defeat the Family.
As all of the X-Men prepare for a festive Christmas, foster child Jubilee is thrilled. She, Storm, and grouchy humbug Wolverine go last-minute shopping in Manhattan, only to be caught in a life-or-death crisis involving Leech, the littlest Morlock. Leech needs blood transfusion, so Wolverine's blood is given and then Leech gets better. Additionally Storm agrees to give back to Callisto her title as the Morlock's official leader.
When Professor X suffers a slight concussion, his powerful psychic mind is suddenly open to manipulation. The Shadow King takes advantage of this and takes possession of Xavier, leaving his mind trapped on the Astral Plane. Jean Grey again traps Shadow King on the Astral Plane, and Professor X regains control of his body.
Shortly after Magneto breaks into the X-Mansion, High Evolutionary and his New Men capture him, Quicksilver, Beast, Wolverine and Scarlet Witch, to do experiments on them. He also reveals that Magneto is Quicksilver and Scarlet Witch's father. The other X-Men later defeat High Evolutionary and His New Men, and save the captured mutants. During this episode, High Evolutionary transformed Wolverine into a werewolf.
Omega Red, the destruction machine from the former Soviet Union and a sworn enemy of Wolverine, is thawed and sent two miles beneath the ocean to salvage a disabled, toxic nuclear submarine threatening to break up near Hawaii. His only condition: Wolverine and Storm go down with him as insurance. Once in the sub, Omega Red reveals his plan to use the missile to cause destruction. Rogue destroys the sub, rendering it unable to launch its warheads. The submarine sinks deeper into the ocean, leaving Omega Red trapped inside.
Part 2. The X-Men are attacked by the Phalanx, a race of techno-organic aliens seeking to assimilate all life on earth. Warlock, Beast, Forge and Mr. Sinister are trying to find help but Magneto at first sees it as his chance to watch humanity go down.
The alien Arkon comes to Earth and begs Storm to return with him to his planet in order to save it from meteorological chaos threatening his people. After much pleading Storm agrees, but leaves a clue for the other X-Men to follow. Once successful, Storm is proclaimed savior throughout this universe, and Arkon asks her to marry him!
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. 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.
Longshot, rebel from another world, tumbles into this world with no memory. It turns out that Longshot is on the run from Mojo, a maniacal inter-dimensional TV executive. Mojo uses Jubilee as a 'prize' to lure Longshot and the X-Men into a deadly contest which Mojo broadcasts 'live' to raise ratings.