Leaving the radical Brotherhood of Mutants and obtaining secret financial backing from the Hellfire Club, Charles Xavier established the Xavier Institute for Gifted Children in New York. He gathered Cyclops, Marvel Girl, Colossus, Storm and Beast as his X-Men, defending mutants while promoting peaceful co-existence with humanity. Iceman joined them after being saved from Sentinels, and Wolverine after the X-Men rescued him from Weapon X.
When the Brotherhood kidnapped the U.S. President’s daughter, the X-Men freed her, gaining the President’s favor and ending Sentinel attacks on innocent mutants. Cyclops briefly defected to the Brotherhood, unhappy Xavier was dealing with “the Evil Empire,” but when Magneto attempted to destroy Washington with reprogrammed Sentinels, Cyclops returned to the fold. Weapon X soon abducted all the X-Men except Wolverine, coercing them to become operatives until the Brotherhood freed them.
When the X-Men were called in to hunt down Xavier’s murderous mutant son David, Iceman was badly injured and Colossus was forced to kill David. Iceman’s parents removed him from the school and tried to sue Xavier, pressured by an anti-mutant senator; however, Iceman refused to co-operate, and dropped the suit. Shortly after Kitty Pryde joined the X-Men, Xavier sent Wolverine and Cyclops on a mission to the Savage Land; while there, Wolverine deliberately left Cyclops to die, jealous of his relationship with Marvel Girl. Meanwhile, the Hellfire Club revealed their true motivations when they tried to merge Marvel Girl with a hostile extradimensional entity, the Phoenix Force.
Magneto returned and the Brotherhood resumed its anti-human terrorism. Implicated as Magneto’s allies since they had falsified reports of his death, the X-Men became fugitives, battling the Ultimates and escaping only due to the surprise return of Iceman. The X-Men located Magneto thanks to Cyclops, who had been found and healed by the Brotherhood. Defeating Magneto and saving Florida from nuclear destruction, the X-Men became national heroes; the White House pardoned them but placed them under the supervision of S.H.I.E.L.D. In the wake of this adventure, Nightcrawler and Rogue were recruited into the X-Men, and Cyclops fired Wolverine. Cyclops later relented, feeling Wolverine’s best chance of redemption was with the X-Men.
The next few months saw a visit to the mansion from Spider-Man, an incursion by remnants of Weapon X, and the addition of Angel to the group. Beast left to join Emma Frost’s rival mutant educational program, but was killed in a Sentinel attack; Dazzler, one of Frost’s other recruits, joined the X-Men, though her rock chick ways irritated Xavier. The serial killer Sinister nearly slew Xavier and Iceman before Rogue defeated him. Believing a worldwide spate of horrendous nightmares might be a telepathic mutant’s distress call, Xavier sent several X-Men to Siberia, where they encountered the Ultimates and learned of the coming of Gah Lak Tus; Xavier subsequently helped oppose the world destroyer.
After Rogue left the team to be with mutant thief Gambit, Xavier sent several X-Men to Genosha to find out if convicted murderer Longshot had been framed by the anti-mutant regime. They learned he was guilty, but not before an unauthorized mission led by Dazzler freed him. The X-Men recently tried to prevent some of Emma Frost’s new students from breaking into S.H.I.E.L.D.’s Triskelion, bringing them into conflict with the Ultimates and Magneto once more.