- Make no mistake, children: We're here to stop a war.
- -- Professor X
Charles Xavier befriended the mutant known as Erik Lensherr, who was to become the mutant terrorist known as Magneto. Eric and Charles bonded over their dreams for the new mutant race. Together, they founded The Brotherhood of Mutants in San Francisco, a place where persecuted mutants could find refuge. A year later, they discovered the Savage Land, a forgotten jungle in the Indian Ocean. In this lost tropical world, Xavier and Magneto built a home for the growing mutant population.
For a time, the two men found the peace they sought, but the partnership began to dissolve as Magneto became increasingly hateful toward mankind, believing Homo superior represented the next step in human evolution, and that Homo sapiens should live under the rule of mutants. While Xavier thought of their Savage Land reprieve as a place to teach mutants, Magneto was merely building a mutant army. The friendship between the two men strained to the breaking point. Xavier and a few of his sympathizers attacked Magneto and made their way to the beach in order to escape the island. Magneto ended the struggle by paralyzing Xavier with a metal spear through the back.
Xavier managed to escape and returned to the United States, where he established his Institute for Gifted Children in Westchester, New York, using his ancestral mansion as a secret base to train his X-Men to use their powers for the benefit of both man and mutantkind. The initially shy and aloof Scott Summers, whose eyes could emit concussive blasts, was the boy scout-like X-Men field leader. Telepathic/telekinetic Jean Grey was outgoing and foxy, but also a very responsible young woman and became the unofficial second-in-command behind Cyclops. Xavier soon expanded the team to include Beast, Storm, and Colossus.
The government-sponsored Sentinels began tracking and killing mutants. Young Bobby Drake ran away from his family in New York to protect them, fearing that the Sentinels would kill him and/or his family if it was discovered that he was a mutant. On their first mission, the X-Men found Bobby alone and scared on a bus in downtown New York City. Before the X-Men could offer Bobby a place alongside them at Xavier's School for Gifted Youngsters, a group of Sentinels attacked.
Just as a decapitated Sentinel was toppling over onto a group of innocent bystanders, Bobby took action and froze the robot in mid-fall, saving the bystanders below. Bobby's heroic act, however, didn't stop the bystanders from hurling glass bottles and bricks at Bobby, the "mutie freak."
At the time, Bobby had a girlfriend. Wanting Bobby to join his team, Professor Xavier erased her from Bobby's memories because Bobby had told her too much about the X-Men and Xavier feared that Bobby would stay with his romance over joining the team. Believing the X-Men - as well as influenced by Xavier - to be a righteous place, Bobby accepted their offer and became an X-Man.
Magneto assigned his elite assassin Logan to infiltrate the X-Men and assassinate Professor Xavier. He was accepted into their ranks, and quickly seduced Jean Grey in order to further entrench himself within the team. However, Wolverine accidentally fell in love with Jean, and was devastated when she left him upon discovering his connection to the Brotherhood. Wolverine eventually betrayed Magneto, abandoning his initial mission and truly joined the X-Men after coming to understand and believe in Xavier's cause. The Professor entered Magneto's mind and turned him into an incredibly powerful electromagnet, which attracted all the Sentinel parts that littered Washington. Using his telekinesis, the Professor shunted Magneto into Earth's atmosphere and exploded the ball of metal. Xavier claimed to have killed Magneto, but had instead secretly brainwashed him, hoping to rehabilitate him.
Seeking answers to Wolverine's past (and to liberate imprisoned mutant test subjects), the team traveled to the site of the Weapon X Project. There they encountered Wraith - and Sabretooth. The scientists of Weapon X tampered with Beast's genetic makeup, enhancing his senses and causing him to grow fangs and become covered in blue fur. Now even more insecure, Hank came to the conclusion that Professor X was using mind control on Ororo to make her love him so he'd stay with the X-Men. This led to a temporary break up between them.
Somehow sensing his father's return to Britain, David Xavier suffered a fatal convulsion but survived by transferring his consciousness into nurse Isobel MacLinden. He fled to the mainland, swapping bodies as each host wore out and slaying anyone who got in his way. He taunted his father, claiming Charles didn't care about him,, and sarcastically suggesting he might join the X-Men as Proteus. Colossus swiftly crushed David beneath a car, apparently killing him.
Katherine "Kitty" Pryde's mutant powers began to manifest, her mother sought help from Professor Charles Xavier. Xavier was eager to have the bright girl, but her mother would only allow her to attend Xavier's school under one condition: that young Katherine would not take part in any X-Men missions, nor train in the "Danger Room." Xavier agreed and Kitty was quickly enrolled in the school.
The Hellfire Club had been keeping an eye on Jean Grey, who they believed to be the Phoenix was reborn. They had secretly funded Charles Xavier's School for Gifted Youngsters to watch over the young mutant until the Phioenix awoke in her. But she briefly went mad and killed Sebastian Shaw.
Jean had began a relationship with Cyclops, leading to a deep rift growing between Scott and Logan. Their rivalry came to a head when Xavier sent the two of them on a mission to the Savage Land, hoping to end their enmity. However, the reverse occurred: Wolverine allowed Cyclops to fall to his death, believing he would then be able to continue his relationship with Jean. Miraculously, Cyclops survived, and returned, revealing Wolverine's hand in his disappearance. Cyclops blasted Wolverine to the ground, and then shocked everyone by offering to let him remain on the team (his only chance of redemption). This experience had a profound effect upon Logan. He realized how badly he had betrayed his friends, and ceased his antisocial, ruthless ways, and even developed a deep and abiding sense of responsibility. He also displayed a protective side for the younger X-Men, namely Rogue, and even eventually formed a bond of friendship - or at least mutual respect - with Cyclops.
For several months the amnesiac Magneto lived peacefully as a Manhattan social worker looking after disabled children; however, the Brotherhood eventually learned he was alive, and restored his memories. Magneto resumed the bombing campaign halted by his errant children, simultaneously gathering every mutant he could into a floating Arctic Citadel. His powers enhanced by a machine of Forge's design, Magneto intended to reverse Earth's magnetic field, leaving humanity to perish in the ensuing environmental chaos. The X-Men stopped him, and he was imprisoned in the Triskelion, home of S.H.I.E.L.D. and the Ultimates.
Xavier was seemingly killed by the time traveling mutant Cable. However, Cable did not actually kill Xavier, but transported his unconscious body with him back to the future to keep under mental block until his questions could be answered. He healed Xavier's spine and replaced his legs and prepared him for the coming of Apocalypse. Xavier tried fighting Apocalypse and failed. He was barely saved when Jean merged with the Phoenix and defeated the powerful mutant. But she pointed out to Xavier that because of him, he set the mutant cause back by a hundred years. She expected him to start over. She reversed time to the point where the attack never happened. He went to Muir Island to recuperate.
As a result of his meddling with Magneto's attempts to punish humanity, Charles was killed: his neck snapped by Magneto.
After the events of Ultimatum, only Jean Grey, Rogue, Storm, Colossus, Kitty, and Iceman were left alive.
After a Nimrod mutant massacre, it was given to the Mutant Resistance a portion of land were to start from zero. They called it Utopia, and managed to make of it a oasis with the help of a sentient seed developed by Blackheat.
Even after a conflict among their own and the useless efforts of the US Army to stop them, the new mutant nation stood strong. When Jean Grey, the new mistress of Tian, failed to convince Kitty Pryde to join her mutant nation, the former X-Woman declared war on Utopia.
The Final Incursion
Together with the Young Ultimates, the X-Men witnessed as S.H.I.E.L.D.'s Triskelion fell at the hands of several heroes who hailed from a parallel universe in retaliation to S.H.I.E.L.D.'s own attacks against their Earth. This clash of realities was the consequence of a phenomenon known as an incursion which ultimately caused both universes to collapse and come to an end together with their inhabitants.
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- Make no mistake, children: We're here to stop a war.