Their arch-nemesis was Apocalypse, and they were instrumental in the battle against the Goblin Queen.

Apocalypse eventually kidnapped Cyclops' infant son, Nathan Cristopher Summers, and infected him with a virus that could not be treated in the present time. The only way save the child's life was to send him thousands of years into the future, where the technology was available to treat the virus. A clan of women rebels from the future, known as the Askani, sent a representative named Jen to the present time in order to bring Nathan Christopher to the future.

Shortly after this, in 1991, X-Factor and the X-Men teamed up to fight one of the X-Men's oldest foes, the telepathic Shadow King. After the draining battle, X-Factor, who were also Professor Charles Xavier's original X-Men decided to move back to his school/mansion where they had all been taught to control their superhuman abilities.

This left the X-Factor comic book without a team to showcase. Rather than end the successful series, Marvel decided to recreate X-Factor with new members, most of whom were already friends or accquaintance of the X-Men or Professor Xavier.

The new team consisted of Havok, Polaris, Strong Guy, Wolfsbane, Multiple Man, and Quicksilver. The new team functioned under the auspices of the federal government, as a group of mutant "police officers" that The Pentagon could call on to battle other superhuman beings, similar to the defunct Freedom Force. Bureaucrat Dr. Valerie Cooper functioned as the liaison between X-Factor and the government and was technically the "leader" of the team despite being a normal human; she wa later replaced by the inventor Forge.

However, this team underwent stress frequently, when Multiple Man was revealed to be under the control of Mister Sinister; Cooper was revealed to be involved with the continued manufacture of the mutant-hunting Sentinels; Quicksilver's marriage rapidly broke apart; Multiple Man apparently died; Strong Guy entered a coma; and Havok went insane. The team was reorganized to include Wildchild, Shard and "former" supervillains Mystique and Sabretooth; the team broke from the government and went into hiding, aquiring new members along the way, but was eventually disbanded when Havok and new recruit Greystone apparently died. Thus, X-Factor was cancelled and replaced by Mutant X.