With the team now larger than ever before, organization suddenly became essential. To remain effective as a group, the X-Men were divided into two squads: Blue Strike Force and Gold Strike Force. Forge, Moira, and Banshee returned to the X-Mansion and act as the team's support staff.
The Blue Squad battled Magneto and his Acolytes in Genosha. Discovering Moira MacTaggart had altered his DNA years ago when he was regressed to a toddler, Magneto questioned if his recent turn to heroics was a result of Moira's tampering or his own free will. Magneto forced Moira to brainwash the Blue Squad into joining his Acolytes on Asteroid M, a space station haven for mutants. To make matters worse, the American and Russian governments decided to use a plasma cannon on the space station to end the threat of Magneto once and for all. Worried about their friends, the Gold Squad sneaked on board and rescued their teammates, while a traitorous Fabian Cortez abandoned Asteroid M and planned to make Magneto a martyr so mutants around the world would join him. Xavier tried to talk the Acolytes into escaping the doomed base with the X-Men, but Magneto and his followers instead stayed to die.
The Gold Squad began their tenure attending a party at the Hellfire Club thrown by Emma Frost. The White Queen explained she and other members of the Club were targets of assassination, and sought the help of her former enemies. Before long, Trevor Fitzroy arrived and began to attack Frost and her Hellions. In Australia, Donald Pierce was attacked by Fitzroy's Sentinels. Gateway teleported Pierce to New York, along with three of the attacking Sentinels. The Sentinels seemingly killed Frost, Pierce, and Jean Grey. Fitzroy drained the life of every Hellion he could subdue, killing all of Frost's students.
Returning her body to the X-Mansion, Xavier realized Jean's consciousness had been relocated to Emma Frost's body. Jean woke up while in the custody of Fitzroy and Shinobi Shaw, who were revealed to be members of the Upstarts. The Upstarts competed in a contest of murder run by the Gamesmaster. Their first targets were former and current Hellfire Club members, and Fitzroy believed he had won and was entitled to run the Upstarts. Jean surprised the two by using telekinesis, a power Emma Frost lacked, and escaped with the X-Men. Fitzroy used the Hellions life essence to open a portal to the future and brought some allies. Bishop, a mutant born in the 21st century, arrived instead. Fitzroy escaped, and Bishop joined the present day X-Men. Xavier realized the White Queen's psyche also remained alive, and returned it to her own comatose body.
Battles with Omega Red (a member of the Soviet Super Soldier program) and Hazard followed.
The two teams were brought together when Professor X was shot while giving a speech during a Lila Cheney peace concert. Stryfe (disguised as Cable) shot Xavier and infected him with a technoorganic virus. Simultaneously, Cyclops and Jean Grey were abducted by the Horsemen of Apocalypse in Westchester. They were delivered to Mr. Sinister, who was disguised as Apocalypse unbeknownst to the Horsemen. Sinister handed the Summers couple over to Stryfe in exchange for a mysterious container.
The Gold Team searched for Scott and Jean while the Blue Team joined X-Factor in hunting down X-Force for information on Cable's whereabouts. Cable convinced Wolverine and Bishop it was Stryfe who shot Xavier and not himself, revealing both were from the future and had long been enemies. Apocalypse woke up from rejuvenation to find he had been impersonated, and was defeated by Stryfe. With Beast and Dr. MacTaggert unable to save Xavier, they were forced to work with Apocalypse. Apocalypse sped up the cycle of the techno-organic virus, forcing the pathogen to burn itself out before it can kill the Professor.
Wolverine received a subconscious telepathic message from Jean, hinting that she was being held captive on the Moon. The X-Men found Stryfe's Moon base and launched an attack. Scott and Jean were rescued, though Cable disappeared with Stryfe into the timestream. Meanwhile, Sinister opened his container to find nothing inside. It was soon discovered that Essex had opened a Pandora's Box with Stryfe's final revenge on the Summers clan; the mutant infecting Legacy Virus.
Following the assassination attempt, the X-Men seemingly dealt with one crisis after the next without a break. Magneto resurfaced very much alive and with a new lead Acolyte: Exodus, the self proclaimed voice of Magneto. Magneto prepared an all out war on humanity upon learning the Magneto Protocols, a plan to alter the Earth's electromagnetic field to inhibit his powers, had been activated. Devastated by his sister's death by the Legacy virus, Colossus lost faith in Xavier's dream and decided to join Magneto and try his.
The rest of the X-Men stood by their mentor and attacked Magneto on his new space base Avalon when he began sending massive E.M.P. waves around the globe. Jean and Xavier attacked him telepathically, while Wolverine defended Quicksilver to save him from his own father. Wounded and furious, Magneto ripped the adamantium laced onto Logan's skeleton out of his body and left him near death. Unable to deal with his old friend's violence any longer Xavier shut down Magneto's mind, leaving him a vegetable. Colossus stayed with his leader, vowing to care for him until he healed.
As Wolverine left the team following his injury, Sabretooth came to stay at the mansion for rehabilitation. A short time later, Scott and Jean finally married. They spent their honeymoon raising a young Nathan Summers in the far future.
Blue Strike Team:
Cyclops
Wolverine
Beast
Gambit
Rogue
Psylocke
Gold Team:
Storm
Archangel
Iceman
Colossus
Jean Grey
Bishop
Supporting Cast:
Professor X
Forge
Banshee
Moira MacTaggert
Jubilee
Former Members:
Revanche
Other Teams:
X-Factor
X-Force
Excalibur
