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 all mutants.
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Mister Sinister and his Nasty Boys kidnap Cyclops and Jean Grey while the X-Men battle Morph at the mansion. Later the X-Men arrive at Sinister's island and fight the Nasty Boys in order to free Cyclops and Jean.
The Shadow King lures Storm home to Mt. Kilimanjaro by 'possessing' her young spiritual son Mjnari, so Rogue and Storm travel to Africa to stop the Shadow King. After a brief fight, Mjnari lures Shadow King back into the Astral Plane and the Shadow King is once again trapped there
Omega Red, the ultimate living weapon, is resuscitated by three corrupt generals who want to reclaim and rule the crumbling old Soviet Empire. Colossus goes to the X-Men for help to save his country and its fragile freedom from these forces of tyranny.
Vindicator and Alpha Flight capture Wolverine. They demand to know the secret of his adamantium skeleton. As Vindicator runs tests on Wolverine, he goes too far and subjects Wolverine to a great deal of pain. At this point the members of Alpha Flight decide that enough is enough and decide to free Wolverine. Alpha Flight defeats the battle droid guards allowing Wolverine, hungry for revenge, to defeat Vindicator. After this, Wolverine sheathes his claws and warns his former comrades to not seek him again.
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. Upon trading Bobby and the tithe for Gambit, Bella gives the Thieves a fake tithe, ensuring their destruction at the hands of the X-Ternal. 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. When the X-Ternal comes, Jean Grey forces a telepathic link with the X-Ternal, forcing her to see the truth. Realizing that she has been duped, the X-Ternal takes away Bella's powers, and the X-Men return home
Time Fugitives begins in New York City, in 3999 AD. Here Time is changing itself. Cable uses his time device and sees that Bishop traveled from 2055 AD to the present to stop a plague, which Apocalypse started. Because he stopped the virus from being created, the antibodies that protected mutants from further plagues were never created.
Cable comes to the present to stop Bishop and save his own future world. After a battle with Bishop and the X-Men he flees. When he checks out the X-Men's biography, he sees that he can use Wolverine's healing power to create the antibodies needed to preserve his future. So, with Wolverine's help, Cable saves both his and Bishop's time line.
Mystique, Rogue's foster mother, forces her to revisit her own past. Rogue's overpowering flashbacks drive her from the X-Men and into the waiting arms of Ms. Marvel, Rogue's first enemy. Her mind is trapped in Rogue's body because Rogue had absorbed her entire mind. On a psychic plane, the vengeful Ms. Marvel and an apologetic Rogue battle it out. Jean Grey uses Cerebro and goes inside Rogue's mind in an attempt to free Rogue from her torment.
Against all odds, Dr. McCoy (Beast) falls in love with Carly, a blind patient of his. Carly's father is a rampant mutant hater until the Friends of Humanity thugs kidnap Carly. Wolverine infiltrates the Friends of Humanity headquarters and meets their leader, Graydon Creed and reveals to the Friends of Humanity that Creed is related to Sabertooth
An alien, Mojo, kidnaps and casts the X-Men as his latest all-galaxy television hit. They are cast in a gladiator-type series where they confront enemies till one side is destroyed, but Longshot betrays Mojo and frees the X-Men. The X-Men destroy Mojo's studio and they are sent back to Earth. Meanwhile, Xavier and Magneto witness Sauron kidnapping Shanna in the Savage Land.
A captured Xavier and Magneto are the bait as Mister Sinister lures the other X-Men to his fortress in the Savage Land. After capturing the team, Sinister plans to use their genetic material to update Magneto's lowly band of "Mutates" to create his own army of unstoppable mutants
Upon touchdown in the Savage Land, the X-Men's mutant powers have been neutralized by Sinister's machines and they are immediately captured by the Nasty Boys and Mutates. Wolverine escapes and teams up with native Ka-Zar. The two travel to the citadel in an attempt to defeat Sinister and free the X-Men and Shanna, Ka-Zar's beloved.