The X-Men are a group of mutants founded by Professor Charles Xavier. Due to a sudden leap in evolution, Mutants, or Homo Superiors, are born with superhuman abilities which generally manifest themselves at puberty. Mutants are often hated and feared by humans because they are different. As a response Xavier created his School For Gifted Youngsters to provide a safe environment where mutants could learn to control their powers. The X-Men fight for a future where humans and mutants could live together in peace.
Xavier's first class of students consisted of the bouncing Beast, the high flying Angel, telepath and telekinetic Marvel Girl (Jean Grey), the young Iceman, and team leader Cyclops. After training extensively in the school's Danger Room, the students were sent on field missions to protect the world from dangerous mutants who would use their powers against humanity. The first such mission brought them to Cape Citadel, Florida in direct confrontation with the master of magnetism, Magneto, who would go on to become their most frequent enemy along with his Brotherhood of Evil Mutants.
The Brotherhood of Evil Mutants disbanded after Magneto's capture by the cosmic entity called the Stranger., The X-Men went on to face new menaces, such as the unstoppable Juggernaut and the robotic Sentinels before Magneto returned again. Their next major opponent was the mysterious organization known as Factor Three. Following the defeat of Factor Three, the X-Men faced their greatest tragedy when Professor X apparently died at the hands of Grotesk. Shortly thereafter, Magneto and his Brotherhood captured the X-Men, and only with the help of the Avengers were they able to defeat him.
After returning home, the FBI's Agent Fred Duncan ordered the team to break up, to better combat crime, which they did for the next few adventures. They were brought back together again by a robot duplicate of Magneto and Mesmero's capture of Lorna Dane, and remained together after defeating them. Shortly thereafter they attended Scott's brother Alex's graduation, only to get involved in a strange caper involving the Living Pharaoh. Alex was apparently lost in the Sahara following this, but the X-Men had little time to search for him before they were attacked by a new incarnation of the Sentinels. Defeating the Sentinels, resulting in the death of Larry Trask, the X-Men searched for a way to help Havok control his awakening mutant powers, only to discover Sauron. This battle led them back to the Savage Land, where they again battled Magneto and his Savage Land Mutates.
The X-Men subsequently managed to stop Sunfire in a battle which caused him to see the error of his ways. It was then discovered that Professor X was not dead at all, but had been preparing for the invasion of the Z'Nox and needed the time without distractions that his death bought him. The X-Men repulsed this threat, and then tracked down the Hulk in order to get a device designed by Bruce Banner to aid their comatose mentor.
Later, the Beast left the team and eventually joined the Avengers.
When the first group of students were captured by the living island of Krakoa, Xavier recruited an all new, all different group. The German demon-looking teleporter Nightcrawler, Russian strongman Colossus, Irish sonic screaming Banshee, African "Goddess" of weather Storm, Japanese hothead Sunfire, Canadian berserker Wolverine and Native American Thunderbird rescued the original team. The new multi-cultural squad set the tone for future generations of X-Men. Soon after, all of the original X-Men left except for Cyclops. Sunfire abruptly quit. Thunderbird was killed during the new teams second mission against Count Nefaria.
Upon reentry to Earth after a mission in space against Stephen Lang's Sentinels, Jean Grey pushed herself to the limit holding their spacecraft together and shielding her team members from intense radiation. Believed dead upon their crash landing in New York's Jamaica Bay, Jean suddenly arose from the ocean calling herself Phoenix and wielding more power than ever before. Unknown at the time, Jean had been replaced by the cosmic entity known as the Phoenix Force, while Jean was placed in a cocoon at the bottom of the bay while her body healed from radiation poisoning. Soon after, the X-Men returned to space to aid Lilandra Neramani of the Shi'ar stop her mad brother D'Ken from using the power of the M'Kraan Crystal to take over the universe. With the crystal about to shatter and destroy reality itself, Phoenix used her awesome power to fuse it back together. The X-Men returned to Earth, and Lilandra briefly returned with them.
After a fight with Mesmero and a fierce battle with Magneto inside an Antarctic volcano, most of the X-Men found themselves in the Savage Land and separated from Phoenix and the Avenger Beast, with each group presuming the other dead. Phoenix and Beast returned to the school to give Xavier the bad news. Having nothing to keep him on earth, Xavier chose to accompany Lilandra back to Shi'ar space.
The X-Men slowly made their way home after their adventures in the Savage Land and in Japan Banshee injured his vocal chords during a battle with Moses Magnum, leaving him powerless. The X-Men were ambushed by Alpha Flight on the way back to the states, who took Wolverine into custody (although he quickly escaped). When they finally returned home, they found Professor X gone and the mansion's telephone disconnected.
The X-Men and Phoenix were reunited at Muir Island when they battled Proteus, the reality altering mutant son of Moira MacTaggert. Despite his injuries, Banshee still accompanied the X-Men for the mission. However. realizing he wanted to stay by Moira MacTaggart's side, Banshee left the X-Men to be with her.
Professor X returned to earth in time to recruit Kitty Pryde for the school and defeat Emma Frost. The battle with Frost plus the ambush at the Dazzler's concert alerted the X-Men to the existence of the Hellfire Club.
While Phoenix believed the X-Men to be dead, she caught the attention of Jason Wyngarde, also known as the former Brotherhood of the Evil Mutant member Mastermind, who created a rich "Lady Grey" fantasy world in her mind with his illusions using a device created by Emma Frost. Eventually believing herself to actually be Lady Grey and also consort to Wyngarde, she was easily convinced to become the Black Queen of the Hellfire Club during the X-Men's battle against them. Phoenix broke free from Wyngarde's control when she saw a psychic version of Cyclops being murdered. Unleashing her dark side, Phoenix became Dark Phoenix, used her powers to drive Mastermind insane, destroyed the Blackbird, and abruptly departed from Earth. Seeking to enjoy the same sense of power she had felt inside the M'Kraan Crystal, Phoenix traveled to a distant star and absorbed it's energy. The sun went nova, destroying a nearby planet inhabited by five billion aliens.
Upon her return to Earth, Beast designed a neutralizer to subdue the all powerful entity. Xavier placed mental blocks in her mind to reduce Dark Phoenix's powers and allow Jean to regain control. Aware of the massacre in their Empire, The Shi'ar arrived on Earth demanding the death of Dark Phoenix. Xavier invoked Arin'n Haelar, an irrefutable Shi'ar duel of honor. Knowing her team would win, Lilandra agreed to allow the Imperial Guard to battle the X-Men. Putting up a valiant fight, the mutants fell one-by-one during a long battle on the Blue Area of the Moon. With only Cyclops and Phoenix left standing, Summers was hit by a stray energy bolt. Set into a panic, the mental blocks Xavier placed in Phoenix's mind were destroyed and she was able to utilize her full power. Lilandra ordered Plan Omega, the complete destruction of the Sol system, upon Phoenix's return.
To avert the loss of the entire star system, Xavier ordered the X-Men to defeat Phoenix. Jean regained control once more, only to activate a Kree weapon and committed suicide to avert another disaster. Cyclops deduced it was her plan all along.
After Jean Grey's funeral, Kitty Pryde came to live at the school as the newest X-Man. Cyclops left the team to figure out where his life was going. Storm became leader in his absence. She underwent a trial-by-fire in a desperate battle against Mystique's new Brotherhood of Evil Mutants to save the life of Senator Robert Kelly.
Other notable foes from this period included Doctor Doom, who attempted to romance Storm, and a memorable encounter with Magneto in the Bermuda Triangle. As Kitty destroyed the central computer of his superweapon, Magneto lashed out and almost killed her. Horrified at his actions, Magneto ceased fighting and contemplated how he had become no better than the humans who had massacred his family. This battle re-united Cyclops with the team.
Corsair of the Starjammers returned to Earth seeking the X-Men's aid in stopping a rebellion against Majestrix Lilandra. The Starjammers were framed for kidnapping Lilandra while it was really Deathbird, the Majestrix's sister, in league with the alien Brood. The X-Men discovered the truth, stopped the rebellion against the Shi'ar empire, and reunited Xavier with Lilandra. Cyclops discovered that Corsair was actually his father, abducted by the Shi'ar decades earlier.
Shortly thereafter a television interview with Senator Robert Kelly worried the X-Men, who had FBI connections in their early years, and thus had government files on many of them. Carol Danvers, Wolverine, and Storm infiltrated the Pentagon and uploaded an open-ended virus that erased all references to the X-Men or members of the team. While in the Pentagon, they also encountered Mystique and Rogue of the Brotherhood of Evil Mutants.
The Brood resurfaced abducting the X-Men, Lilandra, and Carol Danvers. Traveling across the galaxy to their home planet, a Brood Queen implanted embryos within them. Interested by Danvers unique genetic code, she was experimented upon and became Binary. Although the X-Men escaped from "Sleazeworld" all seemed lost, as once the embryos matured their hosts would undergo a metamorphosis and become a warrior Brood. Storm was saved by a young Acanti, a large space-faring creature that resembled a whale and communicated telepathically. The Acanti had been enslaved by the Brood and used as starships. With nothing left to lose the X-Men vowed to save the Acanti race. After freeing the Acanti "prophet-singer" soul from the Brood homeworld, the X-Men were healed. Before killing the Brood Queen, Kitty Pryde found the friendly dragon Lockheed who followed her back to Earth.
During the prolonged period when they were abducted by the Brood, Xavier believed that the X-Men had been killed. Moira MacTaggert convinced him to form a new team of adolescent mutants that needed his help in controlling their powers. Unwilling to see more of his students perish, Xavier was only willing to train them in the use of their special abilities rather than sending them out into combat as he had with the X-Men. These New Mutants ended up in many battles regardless, and occasionally aided the X-Men.
The X-Men learned there was one Brood embryo that had not been eliminated, one planted in Professor Xavier during their first contact with the evil aliens. Racing home they found Xavier had already been transformed into one of the Brood while battling the startled New Mutants. Defeated and taken onboard the Starjammer, Xavier's mind was placed in a cloned body.
Upon returning from space, Cyclops left the X-Men for a prolonged period of time. He had met Madelyne Pryor during a trip to meet his grandparents in Anchorage and fallen in love. It was unknown at the time that Madelyne was a clone of Jean Grey, though the resemblance was obvious. The two married, and had a child; Nathan.
Angel briefly rejoined the team, only to be captured by the Morlocks, and taken down into their tunnels to be Callisto's groom. Storm challenged Callisto to combat, without powers and to the death, which she won, securing her leadership of the Morlocks and Angel's freedom.
Two more members soon joined the team. Rogue's Brotherhood of Mutants teammates couldn't help as the Carol Danvers persona she had previously absorbed began to overwhelm her own personality. Xavier agreed to aid the desperate mutant and added her to the roster. Carol Danvers was furious that her friends would allow the girl that destroyed her life to join the team, and left Earth with the Starjammers. Most of Rogue's teammates still held animosity towards her for what she had done as a member of the Brotherhood, but she slowly gained their trust by continually showing her bravery; she nearly died protecting Wolverine and infiltrated the SHIELD helicarrier to rescue Michael Rossi. Later, Jean Grey's daughter from an alternate timeline, Rachel Summers, traveled back in time and joined the team.
Growing from his crisis of conscience, Magneto became an X-Men ally. Captured by Freedom Force while attending a Holocaust memorial gathering, he was put on trial in Paris. Mostly exonerated of charges on account of his second infancy, the trial was unfortunately interrupted by the Fenris twins, who sent Magneto and Professor X for a ride in the Parisian sewers. Half-drowned and near-death from other medical conditions, Xavier convinced his old friend to take his place as headmaster of the institute. Lilandra took him from Earth to recuperate from his injuries. Using the alias of Michael Xavier, Charles Xavier's alleged cousin, Magneto was Headmaster for a long tenure. Magneto was later invited to join the inner circle of the Hellfire Club, an offer which he and Storm decided was worth accepting.
Cyclops returned, but his attempts to regain leadership of the X-Men was opposed by an experienced Storm, now also an accomplished leader even without her powers. Storm defeated Cyclops through martial skill alone - forcing him to surrender by removing his visor. Cyclops left the team. Shortly afterwards, Angel contacted the original X-Men, including a recently discovered living Jean Grey, with the intent of getting them back together again. At the behest of his friend Cameron Hodge, Angel proposed that X-Factor become a mutant-hunting contractor as a cover for their activities. Rachel went dancing up the spiral paths into the Mojoverse shortly thereafter.
The Marauders (secretly commanded by Mister Sinister) made a substantial impact on the X-Men with their callous murder of most of the Morlocks living in the Alley. In their first battle with the X-Men, the Marauders took a gruesome toll, paralyzing Colossus, putting Nightcrawler in a coma, and trapping Shadowcat with her own power such that she was slowly discorporating. Magneto succeeded in healing Colossus, who rejoined the team, but Shadowcat and Nightcrawler were beyond the X-Men's help. Cyclops' brother and reservist Havok, Mojoverse freedom-fighter Longshot, the singer Dazzler, and telepath Psylocke took the injured mutants place. After recovering, Shadowcat and Nightcrawler went on to form Excalibur.
While in Texas searching for Forge, the X-Men battled the Adversary and appeared to die saving Earth on live television. The X-Men did indeed perish but Roma resurrected them , which resulted in them becoming undetectable to electronics. While improving public opinion on the heroism of mutants, their friends and family, including the New Mutants and X-Factor, believed them to be dead. The X-Men maintained this as a cover story to protect their family and friends from the retribution of super-villains, and relocated to the Australian Outback after defeating the Reavers, whose base they claimed. They would also take in Madelyne Pryor to protect her; she was abandoned by Cyclops, and being hunted by the Marauders.
Soon, the X-Men were lured back to New York during the Inferno crisis. Madelyne Pryor was discovered to be a clone created by Mr. Sinister that a part of the Phoenix Force entered after committing suicide on the Moon. Pryor struck a deal with the demon N'Astirh to become the Goblin Queen out of anger at Cyclops. N'Astirh's intentions to sacrifice Nathan to allow demons to freely travel to Earth became apparent as his spells slowly converted New York City into a hellish nightmare. X-Men and X-Factor, after being pitted against one another, defeated the demon. Pryor was suicidal after learning of her origin, and killed herself in an attempt to bring Jean Grey with her. Jean survived, and absorbed the remaining Phoenix essence within Madelyne. This was the first time the X-Men were able to confirm that Jean Grey was alive.
Besides resurrecting the X-Men, Roma gave them a mysterious jewel called the Siege Perilous. The magical gem could enlarge to a giant portal. All who entered would be judged by higher powers, their good acts and ill deeds weighed, and be reborn in a new life without remembering their past lives. The X-Men found no use for the jewel during the Inferno, against the alien Brood, or when returning to the Savage Land. Curious, Dazzler used her powers to take a look inside the illuminated gem. She saw various alternate versions of herself before they were all murdered and merged into a single being that warned Dazzler everyone dies sometime.
Later the same day, a merged Nimrod/Mastermold attacked the X-Men. With only herself and Rogue left standing, Dazzler threw the Siege Perilous behind the Sentinel hoping her enemy would be sucked into the portal. While the portal appeared, the Nimrod/Mastermold anchored itself to the ground and grabbed Rogue as she tried to push it through. With no other choice, Dazzler blasted both of them into the gateway.
With Rogue presumed dead, and other members leaving the team, the X-Men were down to only Havok, Dazzler, Colossus and Psylocke. Back in the Savage Land to rescue Polaris, Psylocke had a precognitive vision of the X-Men dying back in the Australian Outback and a bound Gateway pointing to the Siege Perilous. Worried about her vision, Betsy wasn't able to warn the others before Gateway teleported them back to the Outback.
Immediately sensing the Reavers approaching when they returned to Australia, Psylocke suggested using the Siege Perilous to escape as the X-Men were in no condition to face the deadly cyborgs. After a brief discussion, and telepathic convincing of Havok, all four mutants entered the gateway. As the portal collapsed back into a gem, Donald Pierce arrived and smashed the jewel to pieces.
Meanwhile, Polaris boarded a freighter to travel back home. Her magnetic powers stolen by Zaladane and replaced with awkward size changing and invulnerability, Lorna couldn't simply fly back to her friends. Strangely, she noticed the sailors began to act weird and that her body had become a nexus for negative emotional energy. As chaos erupted on board, Lorna contacted Muir Island for help bringing Banshee to rescue her. Lorna informed all the Muir Island residents that the X-Men were indeed alive, but a sudden siege occurred before anything could be done. A haphazardly created interim group of X-Men was formed to protect allies of the mutants living on Muir Island from an attack by Pierce's Reavers. Lorna joined mutants Forge, Banshee, Multiple Man, Siryn, the Morlock Sunder, X-Allies Sharon Friedlander, Tom Corsi, Alysande Stuart, Amanda Sefton, Legion and Moira MacTaggart to defend the research center. Val Cooper dispatched Freedom Force to assist. Though the attack was repelled, Sunder and Stonewall were killed by the cyborgs while Destiny was murdered by a Shadow King possessed Legion. The remaining "Muir Island X-Men" stayed, under the influence of the psychic entity.
Weeks after entering the gateway, Rogue returned to the empty Australian base with her memory intact. At first believing the cosmic judging was a joke, she realized the memories she contained belonging to Carol Danvers were gone. She was then attacked by Ms. Marvel, and discovered the Siege Perilous had given both personalities within Rogue a body connected to a single life force. Rogue was prepared to die, but Magneto intervened and killed Danvers. The two spent time in the Savage Land, allying themselves with Ka-Zar against Zaladane, and began to become attracted to one another. Their relationship ended before it had a chance to blossom once Magneto killed Zaladane, which Rogue opposed.
After the Reaver assault Forge and Banshee began to look for the missing X-Men, and found Colossus in New York City under the guise of Peter Nicholas. His memory of his superhero life and his special powers gone, Colossus had become a popular artist in Soho living with Genoshan emigrants. Peter even began a relationship with the Morlock Callisto, her face molded in that of a beautiful model by Masque. Realizing he was happy in his new life, his former teammates left him alone.
Psylocke was found naked and amnesiac by agents of The Hand. Her mind and soul were transfered into the Asian body of Kwannon, and she was brainwashed into becoming the Lady Mandarin. On a mission she faced Wolverine, and upon attacking him with her psychic knife the backlash of memories of the X-Men began to break her free from the Hand's control.
Storm, believed killed by the Nanny, had actually been de-aged to a pre-teenager; loosing her memories of her adult life in the process. She was framed for murder by the Shadow King, and went back to being a thief. Eventually she crossed paths with Gambit and the two began a partnership, stealing from the rich and giving to the poor. Found by the Nanny before long, the two defeated her and though Ororo's memories were returned she remained a child. Ororo took Gambit with her to the X-Mansion and reunited with Forge and Banshee as they were on their search for the missing X-Men. Unfortunately, tests proved Storm was stuck without her powers as a prepubescent .
Dazzler was discovered on the beach by Guido, Lila Cheney's bodyguard. Alison learned of her past life through computer files, and became trapped in the Mojoverse after a teleport of Lila's went awry when trying to save Longshot from Spiral.
The partially regrouped team at the X-Mansion was soon thrown another hurdle; Magistrates from Genosha arrived to capture the mutants for crimes committed on the island. Ororo recognized one of the attackers to be Havok, but couldn't warn her teammates before she was defeated along with the New Mutant members Warlock, Wolfsbane, Rictor, and Boom-Boom. All were transported to Genosha by Pipeline and brought before their true captor: Cameron Hodge. Once an X-Factor ally, Hodge actually despised mutants and made a deal with the demon N'Astirh to become immortal, and came to take control of the nation. Warlock, already weakened, was able to help his friends escape. Hodge intended to acquire Warlocks transformation powers, but Wolfsbane returned to stop the transfer though Warlock wass already dead. Rhane was recaptured, and transformed into a mutate.
X-Factor joined the remaining New Mutants and interim X-Men, consisting only of Gambit, Forge, and Banshee, on a rescue mission to save their friends. In South Asia Wolverine, Psylocke, and Jubilee heard of their friend's fates on the news and ended up rescuing Boom Boom and Rictor. Jubilee tended to the young mutants, while Logan and Betsy infiltrated Hodge's citadel only to be discovered by Havok. The X-Men and X-Factor fared no better, with both squads becoming captives. When Havok saw his brother defeated by Hodge, Alex remembered his life before entering the Siege Perilous. Meanwhile Storm had taken Genegineer David Moreau, creator of the mutate process, hostage but was defeated by Hodge and forced to become a mutate.
A mock trial found the mutants guilty, and all were given the choice of being transformed into a mutate or death. They chose death, but Hodge first had to deal with the insurrection of the Genegineer, aware Hodge's actions were insane, and many magistrates including Wipeout. As Wipeout had canceled most of the X-Team's mutant powers, Hodge killed him hoping they would be permanently lost. Unbeknownst to Hodge, Moreau gave Storm the ability to return the mutants their gifts rather than into a mutate. A rebel magistrate brought Storm to the X-Men and as she used her powers, Ororo reverted back into an adult and regained her powers. Ororo then restored her teammates abilities, and all escaped and started hunting for Hodge.
Concurrently, Moreau planted a bomb to destroy all laboratories within the citadel. Furious, Hodge killed the traitor, though the Genegineer was able to weaken him considerably. The X-Men eventually found their enemy and attacked. Cyclops and Havok unleashed a powerful assault destroying all but Hodge's head which falls near Wolfsbane, who rips it to pieces in a rage. Rictor caused tremors to finally destroy the citadel, burying the remains of Hodge's broken body.
Chief Magistrate Anderson led a revolt against the Genoshan government, and the Magistrates were able to seize power. Havok and Wolfsbane choose to stay behind and make sure mutants were given fair treatment. Because of the intense media coverage of the Genoshan disaster, the world learned the X-Men were still alive. Regardless, the reunited mutants returned to Salem Center and began to rebuild the team that had been splintered for months. Upon their arrival, Warlock's ashes were spread over Doug Ramsey's grave.
Unfortunately, there was no rest for the X-Men. Soon after Xavier returned to Earth from his adventures with the Starjammers, an old enemy returned. The Shadow King had been spreading waves of hate around the globe, and used Polaris to absorb the negative emotional energy to empower himself to unthinkable levels. Professor X used Cerebro to identify the source of the chaos. He returned from his sojourn in space and sent the X-Men to Muir Island to confront their oddly acting allies. It seems Moira MacTaggart had been training the "Muir Island X-Men", and new visitors Rogue and Lila Cheney had taken up residence and participated in duels. When the mutants arrived to investigate, they were surprised and defeated by the Shadow King-controlled island residents.
Back in Westchester, Stevie Hunter was attacked by a possessed Colossus. Xavier found no way to break Shadow King's control over him other than erasing the Peter Nicholas personality completely. Charles then asked his original students, X-Factor, to rescue the current X-Team. On Muir Island, Shadow King used Legion as his human host after the current one was killed while Forge eluded possession and even freed some of his friends. The remaining heroes in good mind were divided into three teams, focusing on an astral plane attack on Farouk with a second team defending Xavier from physical attacks and a third freeing Polaris and disrupting their enemies' nexus.
Forge succeeded in using a neuro-synaptic weapon on Psylocke so she could use her "psychic-knife" on Polaris to destroy Farouk's nexus. Xavier was badly wounded during the battle, his legs broken and again confined to a wheelchair. As Shadow King disappeared, Legion fell into a coma and the devastation of Muir Island was apparent. Most importantly, all five X-Factor members returned to the X-Men along with Rogue and Colossus; after many years the X-Men had finally reunited as one team.
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:
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.
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.
Not long after, the X-Men faced with the Phalanx. The Phalanx, a techno-organic race bent on ruling the world, took over the X-Mansion and assumed the form of various X-Men. Banshee managed to escape along with the captive Sabretooth, a recovering Emma Frost, and the youngest X-Man Jubilee. Banshee learned the Phalanx were after the next generation of mutants, hoping to experiment and eventually absorb the young mutants into their collective. Sean and Emma saved the targeted young mutants, but only with the sacrifice of the young Blink. The surviving teenage mutants became Generation X and were taught how to use their mutant powers by Banshee and Frost at the Massachusetts Academy.
Around this time, the Blue and Gold squads dissipated into one large X group. Legion woke up from his coma with his fragmented mind completely healed. Wanting to make up for the pain he had caused his father, David Haller planned to travel back in time to kill Magneto; eliminating the greatest threat to human/mutant coexistence and fulfilling his father's dream. Bishop, Storm, Iceman, and Psylocke traveled back in time to stop him, but were defeated. As Legion fired a powerful psi-blast at Magneto, Charles Xavier sacrificed himself to save his friend. With his own father dead, Legion faded away along with the rest of the X-Men. Only Bishop, a temporal anomaly, remained unaffected. In the present day, a crystalline wave emerged from the M'Kraan Crystal and eliminated all of reality.
Legion's altering of the timeline was devastating. Noticing the mutant energies during the battle against Haller, Apocalypse began his world domination a decade earlier than he would've otherwise. Rather than be defeated by X-Factor, Apocalypse and his Horseman conquered all of North America in a world known as the Age of Apocalypse. He erected a citadel on Manhattan Island with breeding pens and ghastly experiments run by Sinister and Dark Beast, a twisted version of Hank McCoy. Humans fled to Europe, and were frequently massacred by Sentinels. In this reality, the X-Men were created by Magneto and acted as freedom fighters. Although they suffered many casualties, the X-Men were able to send Bishop back in time to stop Legion and restore reality to normal. Somehow four Age of Apocalypse individuals crossed over to the normal 616 reality: (X-Man, Sugar-Man, Dark Beast, Holocaust), while two (Blink and Sabretooth) joined the dimensional hopping Exiles.
When the Professor shut down Magneto's mind months earlier, Magneto's anger combined with Xavier's repressed negativity resulted in the birth of a psychic being. Lying dormant, Xavier's increased frustration with anti-mutant sentiment, deaths due to the Legacy Virus, and the failing of his own students led him to the breaking point. A young mutant was murdered outside the grounds of the Institute by an angry mob. This final failure of Charles Xavier awakened the near-invulnerable entity: Onslaught.
Concurrently, Rogue discovered the enigmatic Joseph. At first she believed him to be Magneto playing dumb, but realized he was truly amnesiac. Concluding he must be Magneto without any memories, Rogue brought him to the X-Men.
Using Xavier's body, Onslaught aimed to turn the human race into a collective. Seeking more power, he absorbed the powerful mutants Franklin Richards and Nate Grey. Erecting a citadel on Manhattan Island and closing it off from the rest of the world, Onslaught used Sentinels and mutant minions to battle the rebelling heroes. A first strike by the combined might of the Avengers, Fantastic Four, and the X-Men freed Xavier from the entity's control and left him as psionic energy contained within special armor.
Jean Grey aided the Hulk in destroying Onslaught's armor. Thor flew into the now unprotected psionic energy being and managed to damage him. Surmising mutants would only empower Onslaught, the other non-mutant members of the Avengers and Fantastic Four followed and successfully destroyed the entity while seemingly sacrificing their own lives. In actuality, Franklin Richards had used his reality warping powers to transport them to a pocket universe. No one discovered the fate of the heroes for a while, and in the meantime anti-mutant hysteria erupted into chaos. Professor Xavier was taken into federal custody.
The mysterious Bastion used the Onslaught crisis to push his militant anti-mutant agenda to the United States government. With the nations approval, Bastion's Prime Sentinels hunted down and eliminated mutants across the country under Operation: Zero Tolerance. Cannonball, Wolverine, Cyclops, Jean Grey, and Storm were captured along with members of Generation X, though all managed to escape. The Xavier Institute was completely ransacked, though Cable was successful in protecting the mansion's extensive computer systems.
In New York City, Iceman managed to save Dr. Cecilia Reyes (a mutant with a psioplasmic force field) from termination, though her genetic secret was exposed. The bone-wielding Morlock Marrow and Israeli mutant Sabra joined the two and took the confrontation to Bastion himself. Before the matter could worsen, Senator Kelly was brave enough to put an end to the murder and SHIELD arrived to arrest the madman. A short time later, Bastion was revealed to be the Nimrod/Mastermind robot upon emerging from the Siege Perilous.
Meanwhile the other X-Men returned from a space journey to aid the Shi'ar, and Bishop was separated from his teammates along with Deathbird. The rest ended up prisoners of the Nanny, and were eventually brought before Erik the Red (a disguised Magneto) who put Gambit on trial for past crimes. Erik revealed Gambit led the Marauders to the Morlocks during the "Mutant Massacre". Repulsed, Remy's friends abandoned Gambit half-naked in Antarctica. Returning home, the remaining X-Men helped save Cyclops from Bastion's last laugh; a bomb planted in his chest.
Dr. Reyes, Marrow, and Maggott (a mysterious mutant met by Psylocke and Angel with intestines that became giant maggotts) stayed at the Institute and joined the X-Men. The Summers left for Alaska so Scott could recover from his wounds, leaving Storm and Wolverine in charge. Rogue, Joseph, Psylocke, and Cannonball also remained. The new team only existed briefly, battling Alpha Flight and extradimensional demons. Shadow King returned to trick Psylocke into giving him control of every mind on Earth, and all telepaths briefly lost their powers. Betsy managed to defeat him, though she could not use her telepathy so as to keep him prisoner.
With the disbanding of Excalibur, former X-Men Shadowcat, Nightcrawler, and Colossus returned to the team and began an era of change. Dr. Reyes set up practice in Salem Center, opting out of the superhero life, while Maggott briefly joined Generation X. The new squad faced a seemingly alternate group of X-Men lead by Professor Xavier, though they were actually created by a sentient Cerebro Confiscated by Bastion, the nano-technology used to cleanse the Institute gave the mutant locater artificial intelligence. As the X-Men tried to solve the mystery, they found the real Xavier and brought him back to Westchester.
Unexpectedly, Magneto resurfaced once more. Holding the Earth hostage with the planets electromagnetic field in his control, the X-Men traveled to his Antarctica base. Joseph was discovered to have beeen a clone created by Astra (an old foe of Magneto and member of the original Brotherhood of Evil Mutants), who was supposed to kill his genetic brother but his amnesia got in the way. In the end, Joseph sacrificed himself to stop Magneto. Yet, the United Nations gave into Magneto's demands anyway; Magneto was handed the island of Genosha.
Logan was kidnapped by Apocalypse and forced to fight the savage assassin Sabretooth for the mantle of the Horseman Death. Knowing that he might be able to resist Apocalypse's programming and that Sabretooth would be a very dangerous villain with the support of Apocalypse, Logan fought and defeated his nemesis. As a result, his skeleton again was laced with Adamantium. Meanwhile, a Skrull imposter took Wolverine's place with the X-Men. Under the control of Apocalypse, Wolverine fought the X-Men ferociously in his Death persona. But with the help of his teammates, he eventually broke free from Apocalypse's control.
Apocalypse finally revealed the secret of "The Twelve", a dozen mutants prophesied to defeat him. The X-Men tried to round up the mutants listed as the twelve according to one of Destiny's diaries. With the help of Skrulls and his new Horseman, Apocalypse managed to capture them first and admited he was the one who started the rumor of mutant saviors; He instead planned to absorb the powers of "The Twelve" to become invincible and unveil the Age of Apocalypse. Using Nate Grey as a vessel for intense energy, the Living Monolith acted as a power conduit transferring the power of the other mutants: Storm, Sunfire, and Iceman (the forces of nature); Magneto and Polaris (opposing magnetic poles); Bishop and Mikhail Rasputin (time and space); Cyclops, Cable, and Jean Grey (familial unit); and Xavier (mind). Apocalypse did not factor in Magneto's weakened powers, which broke the machine used for the power transfer and freed the twelve. Nate Grey was still in danger of being possessed by Apocalypse, so Cyclops decided to free Nate and take his place. With no sign of their former friend, the X-Men destroyed Apocalypse and Scott was presumed dead. Cable joined the X-Men following his father's apparent death.
Soon after, the High Evolutionary was manipulated by Sinister to revert all mutants back into humans. The X-Men temporarily enjoyed normal life, but their powers returned shortly. Six months passed, and the Neo emerged. Claiming to be the next stage in evolution after homo sapiens superior, they were also effected by the High Evolutionary's actions and suffered casualties. The Neo battled the X-Men several times. Dr. Reyes was brought back into the X-World temporarily. The Neo eventually yielded to Magneto, who was preparing to wage war on humanity.
Meanwhile, Senator Robert Kelly was running for President on an anti-mutant platform. Sage attempted to persuade him from causing a race war, but he remained headstrong. Mystique again attempted an assassination along with her Brotherhood, but made her actions much more obvious. The Brotherhood's attack on Kelly was prevented by a dying Pyro, who begged the Senator to stop the circle of violence. Kelly began to think twice.
Mystique's real intentions were more sinister; she had tampered with the Legacy Virus to release a strain that would only infect regular humans. During the attempt on Kelly's life, Mystique and Sabretooth attacked Muir Island where Dr. MacTaggart had finally discovered a cure of the virus. Mystique neutralized Wolfsbane's powers as she tried to defend her mother, whom Mystique mortally wounded. Mystique even stabbed her own foster daughter Rogue attempting to keep the cure hidden, yet Rogue recovered quickly enough and subdued her. Professor Xavier was able to transfer Moira's knowledge of the virus to his mind before she died. As Cable aided his mentor, a human angry at Senator Kelly's change of stance on mutants shot and killed him.
Beast used Moira's data to create the Legacy Virus cure. Unfortunately, a mutant power signature had to be activated for the cure to disperse around the world. Impatient for Dr. McCoy to discover another way, Colossus injected himself with the cure and activated his mutant power; killing himself but saving the lives of countless mutants.
Jean Grey still couldn't believe Cyclops was truly dead, and went on a journey with Cable to discover the truth. The two eventually found Scott in the Middle East using Jean's rapport with her husband. Cable used his psimitar to cleave Apocalypse's final hold on his father. Returned to his friends, Cyclops became more distant and self-conscious due to insecurities from being possessed. His marriage deteriorated, and eventually led to him seeking comfort from Emma Frost.
With the Legacy Virus cured, the mutates on Genosha were healthy enough for Magneto to amass a superpowered army. At a time when Storm was away, leading a squad of the X-Men in search of Destiny's diaries, and many others having left for personal reasons, Magneto went after Xavier. Without enough powerful X-men around to stop him, Magneto was sucessful in his attempt to capture Xavier, whom he brought to Genosha on the eve of his invasion. Cyclops and Wolverine infiltrated the island nation as Jean Grey recruited ex-Alpha Flight member Northstar, along with Wraith, Paulie Provenzano, and Sunfire's sister Sunpyre, convincing them to join an interim X-Men team. Dazzler showed up seeking help but also joined the group, and Jean mentally controlled the Acolyte Joanna Cargill to aid the team. On Genosha, the team managed to free Xavier who mentally stopped Magneto from ripping out Wolverine's adamantium a second time. Convinced there was no other way, Logan impaled Magneto.
The X-Men were again divided into squads, this time under different circumstances.
Not trusting Xavier or anyone else with knowledge of the future of mutantkind, Storm secretly gathered a squad to obtain the prophetic diaries of Destiny. The team left the safety of the Institute and became mobile. Early on, Psylocke was killed and Beast was critically injured by Vargas. Australian siblings Lifeguard and Slipstream later joined in the quest. Eventually the team abandoned the search after realizing the prophecies only came true if they chose to let the diary control their actions.
The "Away Team" of X-Men had their own problems to deal with, confronting Banshee's paramilitary X-Corp, an organization created to patrol the growing mutant population. Sean formed the team in his grief after Moira's death. Mystique was disapproving of his use of some villainous mutants against their will. She infiltrated the X-Corps and slit Banshee's throat, putting an end to the X-Corp. Mutant prostitute Stacy X briefly joined the team after her brothel was destroyed by the mutant hating Church of Humanity. Later, a reformed Juggernaut, a psychotic Polaris, Northstar, and Havok joined the team.
After the Eve of Destruction crisis, the Massachusetts Academy closed its doors. Professor Xavier requested Emma Frost to teach in Genosha for unspecified reasons. A new nemesis for the X-Men arrived in the form of Cassandra Nova, Xavier's twin sister whom he killed in the womb. The fetal Xavier recognized her as inherently evil, his own personal "mummudrai", and strangled her until she was delivered stillborn. Very powerful, Cassandra remained alive but weak, until decades later when she was finally able to create a psionic body. Cassandra Nova resurfaced in South America and activated a forgotten Master Mold, manufacturing immense Sentinels to attack Genosha. Magneto, alive but paralyzed from Wolverine's attack, could do nothing but watch as the entire island along with sixteen million mutants were exterminated.
Emma Frost appeared at first to be the only survivor due to her sudden mutation of diamond-hard skin. Many mutants around the world began mutating further and gaining new powers. Dr. McCoy labeled them as secondary mutations. Other Secondary Mutations noted were Phoenix's returned telekinesis and Beast's more feline appearance.
Cassandra Nova was brought into custody by Cyclops and Wolverine, but managed to break free at the Xavier Institute and switch bodies with Charles Xavier. In Xavier's body, she shot her previous body to near death. At this point, Emma Frost officially joined the team and the Institute was reopened to students, containing a much larger student body and classes taught by X-Men. On live television, Cassandra Nova-as-Xavier admitted to the world he and all resident at the Institute were mutants, revealing the X-Men's best kept secret. Only the Beast suspected anything was wrong, and Cassandra Nova took control of Beak and had him beat him into a coma before she left on Lilandra's starship for the outer reaches of space.
Jean Grey assumed the role of Headmistress at the Institute and promptly drove off an attack by the U-Men; humans who graft mutant tissue to themselves. During her defense of the school, Jean manifested the Phoenix raptor. Meanwhile, Cyclops and Emma Frost were captured by John Sublime (leader of the U-Men) as he forced Martha the mutant brain to telepathically subdue the X-Men. Both managed to escape, and a freed Martha manipulated Emma Frost into dropping Sublime off of his skyscraper.
Beast finally awoke from his coma to warn his teammates Xavier's mind has been trapped in Nova's dead body. Chinese healer Xorn accepted an invitation to join the X-Men in time for another bout with Cassandra Nova. After wreaking havoc on the Shi'ar Empire, Cassandra Nova fooled the Imperial Guard into attacking the Institute. The X-Men are weakened by nano-sentinels that had been planted by Cassandra Nova, but were cured by Xorn. Jean was able to fragment Xavier's mind with the help of Cerebra, and placed a tiny part in every mutant mind on Earth. As Nova returned to the school and was about to use the mutant locater to eliminate every mutant on Earth, Xavier's mind instead reformed and resumed control of his body. Once again pure psionic energy, Emma Frost tricked Cassandra Nova into entering the body of the synthezoid Imperial Guard member Stuff. Trapped, Cassandra was reeducated and unable to flee. The Imperial Guard noted that 'The Phoenix is coming, and she is terrifying.'
Without purpose, the X-Treme team returned to the Mansion (minus Slipstream, Lifeguard, and Thunderbird). Rogue and Gambit took a leave of absence after their powers were lost. Conflict with Emma and Xavier over the fate of an accused mutant killer quickly drove them away again. Cannonball joined the team before they faced Reverend Stryker and Lady Deathstrike. Storm was soon asked by the United Nations to lead the X-Treme Sanctions Executive (XSE), a government sanctioned and peaceful paramilitary force responsible for policing relations between humans and mutants. The remaining X-Treme members joined along with Wolverine and Magma. Rachel Summers was rescued from Elias Bogan by the XSE, and also joined.
With his secret out, Xavier changed his strategy and created the X-Corporation. With headquarters in many major cities around the globe, the new organization acted in more proactive ways to improve human-mutant relations. Unfortunately, the Paris X-Corp had to stop the menace of an experiment of the Weapon Plus program, with Darkstar dying in the process.
Unrest slowly took over the mansion, when Quentin Quire and his Omega Gang boldly pushed Magneto's policies during "Open Day" as humans visited the Institute. Becoming violent under the influence of the drug Kick, the Omega Gang attacked humans and the intruding X-Men. Sophie Cuckoo, one of Emma's telepathic quintet protégé Stepford Cuckoos, perished using Cerebra to stop the Gang's rampage. The grief of Sophie's sister, Esme Cuckoo, led her to reveal Emma and Scott's psychic affair and shot Frost while she was in her diamond form; splintering her into thousands of pieces. Sage and Bishop's investigation found the culprit, but Esme fled the Institute. Although furious at Emma Frost for becoming close to her husband, Jean displayed vast telekinetic power and reformed Emma's broken body.
Xorn pushed Magneto's theories on his Special Class of young mutants. Disapproving, Xavier confronted him only to discover Xorn was Magneto in disguise. Trapping Wolverine and Jean Grey on the remnants of Asteroid M and incapacitating the other X-Men, he destroyed the Institute and took over Manhattan. Moving closer to the Sun, Wolverine killed Jean so she could unlock the power of Phoenix. Cyclops led a last ditch assault on Magneto and his allies, and Phoenix returned in time to defeat the mad mutant. On several occasions, they noted that something was odd about Magneto, which infuriated him. He made various threats such as ripping out Wolverine's adamantium again as 'proof' that he really was Magneto. Knowing he was defeated, Magneto used his stored energy to give Phoenix a stroke 'on the planetary level'. Wolverine decapitated Magneto in a berserker rage as Jean Grey died in the arms of her husband.
With Jean Grey dead, Cyclops rejected Emma's advances and left the Institute in Beast's hands. Hank couldn't deal with the pressure of running the school by himself, and began taking Kick to deal with the stress. The drug Kick turned out to be an aerosol form of Sublime, an ancient parasitic bacteria that took the human form of John Sublime. Infected by Sublime, Beast created a chain reaction that destroyed civilization. Years later, Jean was reborn as the Phoenix. Although first controlled by Beast, Wolverine and the remaining X-Men restored her memory. After eradicating Sublime, White Phoenix traveled through the timestream and pushed Scott to embrace Emma's advances, averting the disastrous future.
Scott Summers and Emma Frost became co-headmasters of the rebuilt Xavier Institute. The returning students were arranged into squads led by other X-Men. Professor Xavier left for Genosha, and began rebuilding the nation with the help of Magneto; "Xorneto" had been an impostor after all. The XSE made the Institute their headquarters, while the other X-Teams werre rearranged.
The XSE battled the Fury, Savage Land mutates, and a new Hellfire Club. Sage left the team to aid Sunspot in controlling the Club, hoping to prevent Roberto becoming corrupted by power. Cannonball soon rejoined X-Force after recuperating from injuries sustained battling the Fury. Psylocke suddenly appeared alive and well in the exact spot she was murdered. Although surprised, she was welcomed back to the team.
Gambit, Sabretooth, Iceman, Juggernaut, Polaris, Northstar, Rogue, Shen Xorn
The real Xorn briefly joined the X-Team, and helped battle the latest incarnation of the Brotherhood. Towards the end, the Brotherhood members were sucked into the black hole within his helmet. Juggernaut, distraught after the murder of his young friend Sammy by Black Tom Cassidy, willingly entered the void to look after the confused Nocturne (TJ Wagner).
Cyclops' team ditched the leather costumes to bring back spandex, trying to amaze humans and appear more like superheroes. The team faced the extraterrestrial threat of Ord and Genetech's mutant cure. Shadowcat discovered Colossus very much alive within Genetech's Research Facility, and he rejoined his friends. Later, the Danger Room became sentient and tried to murder the X-Men.
The Scarlet Witch lost control of her reality warping powers and destroyed the Avengers in the process. Magneto took his comatose daughter to Genosha, though neither Xavier nor Doctor Strange could help her. With the combined New Avengers and "Astonishing" X-Men arriving on Genosha to deal with Wanda's increasingly worrisome actions, Quicksilver manipulated his sister to create the House of M; a reality where mutants ruled over baseline humans.
Though the world seemed perfect, Wolverine began to suspect something was wrong. With the help of young mutant Layla Miller, the X-Men and other heroes remembered their past lives. The enlightened heroes commenced an attack on Magneto's Genoshan headquarters and tried to find the missing Professor Xavier. Quicksilver's betrayal was revealed, and Magneto nearly killed him. Angry how her mutant heritage and her fathers choices nearly destroyed her family, the Scarlet Witch uttered three words to solve what had happened: No More Mutants.
The world returned as it was, with some heroes remembering the House of M. Immediately, Emma Frost realized something was wrong and used Cerebra to locate mutants. Wanda's powers had erased the X-Gene from many mutants, drastically reducing the homo sapiens superior population from millions down to an estimated 198. Among the depowered were Magneto, Quicksilver, Scarlet Witch, Chamber, Jubilee, Blob, and Beak. Other consequences included Wolverine remembering his past and Professor Xavier being nowhere to be found.
Immediately, the Xavier Institute became a sanctuary for mutants who had nowhere else to turn. Old enemies such as Arclight and Scalphunter joined allies like Outlaw and Erg among the powered mutants who soughy refuge. Emma Frost forced the depowered students and faculty to leave the Institute, including Danielle Moonstar. Afraid of violence breaking out, Valerie Cooper dispatched Sentinel Squad O*N*E to protect the swelling population at the X-Mansion. The X-Corp branch in Paris was bombed, causing the other branches to shut down. A group of rabid mutant haters, the Sapien League, attacked the school, declaring that the events were a 'sign' and that they must kill the remaining mutants.
At a time when the X-Men were needed the most, a few of their oldest members left the fold. Storm decideed to stay in Africa to aid desperate mutants.
Apocalypse returned with Horsemen that were formerly X-Men or allies of the group. He planned to eliminate most of humankind and have the surviving populations fight each other to the death. The X-Men reluctantly worked together with ONE against the threat.
Rachel Summers and her teammates found themselves battling Shi'ar sent to eliminate the Greys, in order to eliminate anyone in that bloodline so the Phoenix force would not pass on to them once they managed to kill the current one holding it. They were then whisked away by Jamie Braddock to battle a cosmic threat.
A mysterious mutant, Vulcan returned to Earth, revealing himself to be Cyclops and Havok's long lost brother. With him came a shocking revelation about Krakoa, the Summers family, a 'lost' team of X-Men, and Professor Xavier's current status. These revelations also cost Banshee his life. The team struggled to deal with these revelations. Professor X assembled a team to follow Vulcan into space.
As the Superhuman Registration Act passed, the question of what was to be done with the remaining mutants living in the United States came into question. Ms. Marvel and Tony Stark attempted to recruit the X-men into the Act, but were quickly turned down when Emma Frost reminded them of how when mutants died by the hands of Sentinels in Genosha and various other genocidal events in their history, the super heroes had turned their backs. Through negotiations with Valerie Cooper and the U.S. Government, mutants were NOT required to register under the Superhuman Registration Act.
Rogue was assigned her own team to make. She chose Cannonball, Iceman, and Mystique. When they rescued Karima and Lady Mastermind, and when Cable ans Sabretooth came to the institute, they joined the team as well. They battled the Children of the Vault, Hetacomb, Pandemic, and the Marauders which ended the team. With Cable believed dead, Sabretooth escaped, Cannonball in a catatonic state, Mystique and Lady Mastermind joining the Marauders, Karima possesed by Malice, and Rogue kidnapped by the Marauders and almost dead, Iceman was the only member left.
Professor X recruited Rachel Summers, Nightcrawler, Warpath, Darwin, Havok and Polaris to participate in a space mission to stop Vulcan from unleashing his powers on the Shi'ar empire. Vulcan revived Emperor D'Ken and married Deathbird. Later, he killed D'Ken and proclaimed himself leader of the Shi'ar Empire. Alex witnessed as Vulcan murdered their father, Christopher Summers. Alex, Lorna, and Rachel Summers stayed in space, joining the Starjammers to lead the resistance against Vulcan and his wife.
The first mutant birth occured since M-Day. The mutant was so powerful, it blew out Cerebra and most of the telepaths at the X-mansion. The X-men jumped to the Alaskan town of the mutant's birth to find that the Purifiers and Marauders had beaten them to it. The entire mutant population was now fighting to either save or kill the first mutant baby. Ultimately, Cyclops agreed to hand the baby over to Cable so he could take her to the future where he could protect her. Bishop betrayed the X-Men and attempted to kill the child. He accidently shot Xavier in the head while aiming for the baby.
With the X-Men disbanded and the X-mansion completely destroyed, Beast returned to destroy the last remaining records of the X-Men and its students along with recovering the mutant known as No-girl.
Professor X was actually very much alive thanks to the intervention of the remaining powered Acolytes. However, his mind was badly damaged and only had contact with the X-Man Gambit.
The X-Men disbanded as they no longer had a leader and their teams had literally fought to the death, suffering heavy casualties. X-Force and X-Factor relocated, the New X-men dissolved and the students sent home, while a new Young X-men team was established. Some X-men remained captive of Emperor Vulcan of the Shi'ar Empire.
With members of the team suddenly falling out of contact, Cyclops and Emma Frost investigated the odd events happening in San Francisco. A mutant known as Goddess manipulated the entire city into thinking it was living in the 1960s. Once the few X-men that were present (Angel, Hepzibah, Iceman, Warpath, Emma Frost and Cyclops), subdued the Goddess, they coincidentally rescued the mayor of the city who offered the X-Men a safe haven.
On the out skirts of the city, Cyclops along with Storm, Beast and various other X-Men re-established and built a home base for the X-men and ALL mutant kind. After a brief battle with a artificially re-powered Magneto, Cyclops, through Emma Frost's telepathic powers, sent a message to all mutants around the world that they now had a place they could call home in San Francisco, re-creating the X-men and Xavier's dream once again.
San Francisco became the target of the Skrull Invasion. The Skrulls were not expecting the X-Men to be in San Francisco. The X-men engaged in Guerrilla tactics to cripple the Skrulls. Beast determined that a modified version of the Legacy Virus would have dire effects on the Skrulls. The X-Men effectively spread the virus to the entire Skrull fleet at San Francisco. Refusing to surrender the Skrulls destroyed themselves. The X-Men marched through the streets, welcomed and thanked by the people of San Francisco.
Beast founded a think tank to help undue the damage done by Scarlet Witch following Decimation to restore the mutant population.
The Californian government proposed a ban on mutant reproduction to control the mutant population. The proponent of the legislation was Simon Trask, brother of Bolivar Trask, creator of the Sentinels, and the anti-mutant group known as Humanity Now. Trask led his supporters on a march across the state and when they arrived in San Francisco, they met many of the new mutants in the city including Lorelei, Hellion, Toad, and various other X-men and the city erupted into a riot. Emma Frost, part of Norman Osborn's Cabal, was asked by Osbourn to keep the mutant population under control, but she failed to do so, the Dark Avengers and H.A.M.M.E.R. soldiers were deployed to quell the riots. As a result, Beast was arrested and detained. Osborn also contacted Frost and placed her in charge of her very own group of X-men, while simultaneously publicly having a wheel-chair bound Charles Xavier ask Scott Summers to surrender for arrest.
Cyclops resisted arrest and retreated back to Graymalkin Industries along with the rest of the X-men as they were forced to battle members of the Dark Avengers. Meanwhile, Emma Frost was introduced to her new team of Dark X-men: Cloak, Dagger, Mimic, Daken, Weapon Omega, and Mystique (posing as Charles Xavier for Osborn's agenda) and per Frost's request, the Atlantean Namor. Frost's X-Men responded to a riot led by her former pupil Hellion, following a curfew Osborn put into effect.
Beast was imprisoned and the real Charles Xavier contacted him, stating that the prison they were in (H.A.M.M.E.R.'s west coast base, a renovated Alcatraz Island) was a place where they planned on depowering mutants. The head of the project: Dark Beast, Beast's polar opposite.
Equipment: Danger Room, Cerebro, Cerebra, Image Inducer Cyber-glasses. Although most X-Men choose to individualize their costumes, standard blue and gold uniforms are available.
Transportation: X-Men Blackbird; the original is still in use and Forge has constructed additional models for each team. An earlier version was the X-Men Stratojet and before that the X-Copter.
Weapons: No standard weaponry. Some members have at times carried weapons as suited their tastes and current team philosophy (Longshot throwing knives, Cable futuristic firearms, Forge self-made firearms, Wolverine and Psylocke Katana, Storm Knife). Wolverine additionally has a weapon he is incapable of removing under normal circumstances (Adamantium claws).
It should be noted that bigotry toward mutants in the world of the X-Men has long been seen as a metaphor for all kinds of prejudice towards others occurring in the real world. Professor Xavier has been equated to peaceful civil rights activists like Dr. Martin Luther King. Conversely, Magneto's extreme views could be compared to modern day religious radicals, or Adolf Hitler, believing himself to be a part of a master race which should dominate or exterminate those inferior to them. Recently, Storm has been forming her own perspective that acts as a middle ground and is analogous to opinions of moderate progressive activists.