The universe of Earth-21993 would mirror that of Earth-616 up until the point when Charles Xavier returned to Earth following imprisonment by the alien Skrulls when they attempted to use him as a weapon against Lilandra and returned to Earth. There he would find human mutant relations in utter chaos: His own X-Men fractured, teammates Havok brainwashed, and Colossus and Dazzler amnesiac, Muir Island under the influence of the Shadow King, and a group known as the Mutant Liberation Front was committing terrorist acts across the world.
Xavier would call a meeting between the X-Men, X-Factor, Excalibur and the New Mutants, telling them that they have all fallen apart. Newly appoint New Mutants leader Cable would take offence to this and tell Xavier that times had changed and the X-Men needed to take a harder line on their enemies. Xavier would admonish Cable, calling him a worse threat than Magneto and order him removed from stewardship of the New Mutants. This would to protests from the New Mutants and ultimately a fight between them and the X-Men, ending with the New Mutants escaping. Contacting Cable telepathically, Xavier would swear to wrest back control of the New Mutants from him, and Cable would respond by telling him he's ready to go to war with Xavier if that's what it will come to. Shortly thereafter while Xavier would be meeting with Cyclops and Marvel Girl, Cable would assassinate them with a bomb, killing all three.
At the funeral, Wolverine vows to get vengeance on Cable and kill him in retribution for murdering Xavier, while Storm believes that Cable should be brought to justice, not murdered. This clash of ideologies would lead to the remaining members of the X-Men to pick sides. Forge, Colossus, Beast, and Strong Guy and others joining Storm; while Psylocke, Havok, Archangel, Iceman, and Jubilee joining Wolverine.
With the death of Xavier, many of the X-Men's foes would capitalize on it to strike back at their enemies. Storm's X-Men would be caught up trying to stop a Genshan incursion on the United States; Apocalypse would target the Scarlet Witch, leading to a battle with the Avengers; The Fenris would attack New York City, and the Mutant Liberation Front attacking the Fantastic Four; Human sentiment towards mutants would target the Morlocks leading to many being slain and the Freedom Force being charged with forcing them back underground. While in the Savage Land Zaladane and her Savage Land Mutates would war on the world to expand the boarders of the Savage Land; Other countries are destabilized by anti-mutant hysteria; Gideon and the Externals would begin taking advantage of the violence; Mr. Sinister would dispatch his Nasty Boys to collect the CEO's of Roxxon Oil, the P.T.L. Club, and the Boy Scouts of America; Sebastian Shaw fearing the worst would begin talks with the President of the United States in restarting Project: Wide-Awake.
Meanwhile, Wolverine's team of X-Men would track down Cable and the New Mutants, in the the battle, Wolverine would ultimately kill Cable who would die telling him that Xavier was a better man than Wolverine because he had the strength of his convictions and didn't let his emotions blindly cloud his mind from the mission. Wolverine would fail to understand the meaning of this. The Mutant Liberation Front would next attack the remains of the X-Mansion, leading to a clash with Storm's X-Men but they would soon retreat. The X-Men would be next attacked by Zaladane and her Mutates, leading to the deaths of Beast, and Nightcrawler and Polaris and ending the X-Men fleeing their base. Watching this destruction would be Magneto, who would decide that now is the time to try and unite the mutant nation.
Magneto would eventually kill Stryfe, taking over the Mutant Liberation Front, and begin accepting other disenfranchised mutants into his army, including members from both Wolverine and Storm's ranks. Magneto would launch an attack on Washington D.C., clashing with many of Earth's non-mutant heroes including the Avengers and the Fantastic Four. As Storm's group would mourn their losses, Wolverine's team would eliminate Mr. Sinister's Nasty Boys, prompting Psylock to leave and find Storm's group.
Magnetos group would win a victory, taking Washington D.C. however the ousted President of the United States would then activate the Sentinels, unleashing them upon America. The Sentinels would be easily held at bay by Magneto's magnetic powers, however they would cut across the country eliminating mutants and other super-human threats that would resist capture. Those who were captured were put in internment camps. The Fantastic Four, New Warriors, and Savage Land Mutates would all be wiped out. Wolverine's group would be decimated, with Havok and Archangel being killed and Ice Man being captured. Wolverine would escape vowing to get revenge, while Storm and Psylock would join with Magneto's group for sanctuary.
As Wolverine would find the beaten Sebastian Shaw, he would collect a device from him that would mask him from the Sentinels. Magneto's over confidence would get the best of him as he would destroy Sentinels that were loaded with nuclear weapons, causing an explosion that would kill everyone in Washington D.C. Wolverine would meanwhile use the device collected from Shaw to break into one of the Sentinel camps and free Ice Man, Sunder, Amphibious, Siryn, and La Bandera and form a new group of X-Men to free the world from the Sentinels rule.
X-Men (Professor X, Storm, Wolverine, Colossus, Banshee, Dazzler, Psylock, Gambit, Jubilee, Polaris, Havok,Captain Britain, Nightcrawler, Pheonix, Shadow Cat, Forge), X-Factor (Cyclops, Marvel Girl, Archangel, Beast, Ice Man), New Mutants (Cable, Cannonball, Boom-Boom, Rictor, Warlock, Sunspot, Wolfsbane), Avengers (Captain America, Scarlet Witch, Thor, Quasar, Hawkeye, Iron Man, US Agent, Sersi, Wonder Man), Dark Riders (Apocalpyse, Tusk, Barrage), Fenris (Andreas Strucker, Andrea Strucker), Savage Land Mutates (Zaladane, Amphibius, Barbarus, Brain Child, Gaza), Fantastic Four (Mr. Fantastic, Invisible Woman, Human Torch, Thing, Ms. Thing, Franklin Richards), Mutant Liberation Front (Stryfe, Dragoness, Fourarm, Reaper, Strobe, Sumo, Tempo, Thumbelina, Wildside, Zero), Freedom Force (Avalanche, Blob, Spiral), Morlocks (Masque, Sunder), Externals (Gideon), Hellfire Club (Sebastian Shaw, Tessa), Shadow King, Nasty Boys (Mr. Sinister, Gorgeous George, Hairbag, Slab), Domino, Quicksilver, Siryn, Strong Guy, Magneto, Daredevil, Spider-Man, Sentinels, Black Tom, Caliban, La Bandera, Dr. Doom, Ghost Rider, Hulk, Puck, Vindicator, New Warriors (Night Thrasher, Namorita, Nova, Firestar)
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