Founded by former X-Men, X-Factor publicly posed as humans who claimed to capture dangerous mutants; in truth, they rescued young mutants to protect and train them. X-Factor hired Cameron Hodge to handle public relations, unaware his bigotry would lead him to generate media hype against the "mutant menace". While they still covertly went into battle as the outlaw mutant X-Terminators, their secret was eventually exposed by Mystique and Hodge's anti-mutant group, the Right. However, after saving New York from an attack by Apocalypse's Horsemen, they were honored as heroes by the public. They continued together during the demonic "Inferno" invasion of New York, temporary transport to a world under Celestial judgment, and attacks by the cybernetic Hodge and his allies in Genosha, the Dark Riders, and more, before rejoining the X-Men following an attack on Muir Island by the Shadow King.
Federal agent Valerie Cooper assembled a new X-Factor for the U.S. government, recruiting Havok as team leader, plus Polaris, Madrox the Multiple Man, Strong Guy, Quicksilver, and Wolfsbane, who struggled with her emotions following recent Genoshan brainwashing. Their activities included fighting Mr. Sinister and a rogue Madrox duplicate; teaming with the Hulk and the Pantheon in the war-torn nation of Trans-Sabal; failing to stop the Mutant Liberation Front from killing a doctor who had developed a way to test unborn children for the mutant gene; protecting State's witness Shrew from Cyber and her former team, Hell's Belles; preventing a revamped Brotherhood of Evil Mutants from recruiting the Genoshan refugee X-Patriots; joining the hunt for Cable after he seemingly shot Professor Xavier; and struggles with mercenary mutant Random, who would be both an enemy and ally. During a trip to Genosha, Madrox (actually a duplicate) contracted the Legacy Virus. Shortly thereafter, Val lost the team's trust due to her involvement with a Sentinel program and was replaced as liaison by the mutant technosmith Forge.
The mutant prophetess Haven cured Wolfsbane of her mutate conditioning but the team suffered their first tragedy with the apparent death of Madrox from the Legacy Virus. As a result, Havok briefly quit the team, and Forge took over as leader. Mutant terrorist Mystique was added to the team by the government, and Strong Guy suffered a heart attack from a power overload, sending him into a deep coma. Wolfsbane quit the team, traveling to Muir Island where she joined Excalibur and was replaced by Wild Child. Next the hologramatic mutant Shard, sister of Bishop, was recruited and the team battled the trickster-god the Adversary alongside Roma. After the government forced sociopath Sabretooth onto the team, Havok seemingly went rogue and formed the Brotherhood. Soon after, both Madrox and Strong Guy were found to be alive, and unwilling members Mystique and Sabretooth rebelled. Forge quit shortly before Havok returned, and X-Factor joined with the time-traveling Xavier Underground Enforcers in a mission to save the future. The X.U.E. members then joined a reorganized X-Factor, including Polaris and Madrox, but the new team was shortlived after Havok was seemingly killed in an explosion, though he was actually shunted to an alternate reality (Earth-1298).
Madrox formed a new X-Factor team, the X-Factor Investigations, a private investigation firm that has no relation with the government, as the previous incarnations of X-Factor. However, Val Cooper is trying to recruit the current X-Factor team, but the team does not agree. Currently, the team is also called simply "X-Factor."