An alien, Mojo, kidnaps and casts the X-Men as his latest all galaxy television hit. He uses his psychic powers to pit them against one another on a far distant planet. But when the superstar of Mojoworld, Longshot, betrays the television tycoon and frees the X-Men, they must trust that the luck of Longshot can get them home safely.

When Mystique forces Rogue to revisit her own past, Rogue's overpowering flashbacks cause her to relive the encounter with Ms. Marvel and drive her from the X-Men. Rogue struggles with Ms. Marvel's thoughts which are trapped in her mind and the two battle it out on the psychic plane.

Xavier and Magneto are held captive by Mister Sinister and are used as bait to the lure the X-Men into an ambush at the Savage Land Castle. After capturing the X-Men, Sinister unfolds a plan to use their genetic material to modify Magneto's lowly band of 'mutates' into more powerful and deadly mutants.

Cable comes to the present to stop Bishop and save his own future world. But after a one-sided fight against Bishop and the X-Men, Cable realizes that they might be too powerful to handle on his own. Looking for an alternative, Cable looks into the X-Men's history and discovers that Logan's healing factor may be the key to saving the future.

It's 3999 AD. in New York City and Nate Summers, also known as Cable is leading a war against Apocalypse and his forces. But when a timestorm appears, Cable discovers that the past is being altered by the mutant known as Bishop and that these alterations will cause the destruction of the mutant race.

Upon touchdown in the Savage Land, the X-Men lose all their mutant skills and are immediately captured by Sinister's Nasty Boys. Wolverine escapes and teams up with native Ka-Zar. The two travel to the citadel in an attempt to free the X-Men and Shanna.

When Wolverine's former love, a Japanese woman named Yuriko, stumbles into the Morlock tunnels, she discovers that an alien treasure is burried somewhere in the area. She lures Wolverine and the X-Men into the tunnels with hopes that she can use their abilities to uncover the treasure.

Gambit is forced to return to his southern roots by an ancient tithe, an old family feud and the kidnapping of his brother, Bobby. Bella Donna of the Assassin's Guild uses the kidnapping to lure Gambit into her clutches and force him into completing the aborted marriage. Fortunately for Gambit, the rest of the X-Men follow him back to the bayou; with Gambit's help they successfully confront the Assassins at the designated place and time and expose their deception.

Yuriko's alien discovery, a Shi'ar vessel, turns out to be a prison cell containing a voracious, gaseous prisoner, the M'Kraan Spirit Drinker. It immediately sucks life out of Yuriko and her cohorts, the Reavers, and turns its attention to the X-Men. The X-Men must change their strategy to defeat an enemy they can't touch.

Vindicator and Alpha Flight capture Wolverine and demand to know the secret of his Adamantium skeleton. As Vindicator runs tests on Wolverine to try and replicate his indestructible skeleton, the members of Alpha Flight realize that the experiments are going too far and fight to release him. With an enraged Wolverine freed, Vindicator and Alpha Flight are in for a fight they will never forget.

A Shi'ar emissary, Erik the Red, violently takes over the Eagle One space station. The X-Men race into space to save the astronauts on board and battle Erik the Red. But on the way back to Earth, an energy wave collides with their aircraft. With no other options, Jean takes matters into her own hands and pilots the plane while shielding the rest of the X-Men, exposing herself to the Phoenix Force!

Omega Red, the ultimate living weapon, is resuscitated by three corrupt generals who want to reclaim and rule the crumbling old Soviet empire. Colossus approaches the X-Men for help to save his country from these forces of tyranny. With the help of Darkstar and Colossus, the X-Men must defeat the seemingly unbeatable Omega Red and restore peace in Russia.

When Jean Grey's psycho-kinetic shield fails, she is possessed by the Phoenix Force. Meanwhile, Xavier goes to Muir Island to recuperate after his mind is attacked and a psychic projection of his dark side attacks the X-Men. An alien named Lilandra Neramani comes to assist the X-Men but is taken captive by Juggernaut and Black Tom!

The Shadow King lures Storm home to Mt. Kilimanjaro by 'possessing' her young spiritual son Mjnari. Rogue and Storm must travel to Africa to stop the Shadow King and find a way to lure him back into the Astral Plane.

Mister Sinister and the Nasty Boys kidnap Cyclops and Jean Grey, while the X-Men battle Morph at the mansion. After finally defeating Morph, the X-Men arrive to Sinister's island and must fight the Nasty boys in order to free Cyclops and Jean.

The X-Men elicit the help of a fellow mutant, Banshee, and launch an attempt to save Lilandra. Bet when they arrive at the site, the X-Men are stopped in their tracks by the Gladiator. Faced with a foe unlike any they've seen before, the X-Men are soon overpowered, but not before the Phoenix comes to their aid!

Jean Grey, using the Phoenix's powers, transports all the X-Men to Lilandra's ship where the Empress has hidden the M'Kraan Crystal. While there, a group of super-powered beings named the Starjammers attack and steal the M'Kraan Crystal in order to use it to get close enough to D'Ken to assassinate him. But when the Starjammers set their plan into motion, D'Ken gains possession of the Crystal and unleashes its terrible power.

As Jean Grey and Cyclops attempt to tie the knot, Mister Sinister uses a brainwashed Morph to lay traps to destroy the X-Men one by one. Meanwhile, Graydon Creed begins exterminating mutants in an attempt to rid humanity of all homo-superiors.

D'Ken gets pulled into the M'Kraan Crystal, and becomes one with the universe inside it. Now with unlimited power, D'Ken has become and unstoppable force. With the help of the Starjammers, the X-Men hold nothing back in a fight to defeat D'Ken. Overpowered by their foe, the X-Men face their final moments, but are saved by Jean Grey and the Phoenix!

Magneto brings Senator Kelly to a sunken ship to kill him, in hopes that a war between the mutants and humans will begin as a result. But when the Sentinels locate the senator, they abduct him and bring him to Master Mold who has begun to initiate a plan to replace all the minds of world leaders with computer chips. The X-Men race to save the Senator who eventually realizes that not all mutants are dangerous to the world.

The X-Men stop the time-traveling mutant named Bishop from shooting Gambit and travel to Washington after uncovering the Brotherhood's plans to assassinate Senator Kelly. There, the X-Men discover that Mystique has been posing as Gambit and is really the suspect that Bishop is after! Now, the X-Men must defeat Mystique and the Brotherhood in order to stop the chain of events that will lead to the desolate and violent future that Bishop came from.