The Brotherhood of Mutants is a group dedicated to the cause of mutant superiority over humans. Throughout its various incarnations, the Brotherhood's agenda has gravitated towards either subjugating the human race to the will of mutants or eradicating humanity altogether. Magneto formed the Brotherhood of Evil Mutants, including Astra, Toad, Quicksilver, Scarlet Witch, and Mastermind, shortly after the public debut of the X-Men. After a falling out with Astra that led to her quitting the team, Magneto had the Brotherhood initiate an attack upon humans that was thwarted by the X-Men. Magneto then attempted to recruit the thunder god Thor into his Brotherhood, but Thor refused. The Blob was the next candidate for recruitment, but ultimately declined to join after seeing the way Magneto mistreated his followers. Mastermind then sought to recruit Unus the Untouchable; however, he was blackmailed by the X-Men into declining the offer in exchange for reversing his then-amplified powers. During an encounter with the enigmatic Stranger, Magneto and the Toad were captured and taken to the Stranger's homeworld, shortly after which Quicksilver and the Scarlet Witch joined a revamped version of the Avengers led by Captain America.
After a tenure with the subversive organization Factor Three (intended to become a third major world power), Blob, Mastermind, and Unus banded together as a new Brotherhood. Following a failed attempt to settle the score with the X-Men, the trio were able to make the Beast believe he had killed the Avenger Iron Man and manipulated him into joining until he realized the truth and single-handedly defeated them. Eventually returning to Earth, Magneto re-formed the Brotherhood with Blob, Mastermind, Unus, and the Savage Land Mutate Lorelei to assist him in the creation of a being with unlimited power that he dubbed Alpha, the Ultimate Mutant. In an encounter with the Defenders, the rapidly evolving Alpha unleashed his powers, reducing the Brotherhood to a state of infancy. Subsequently restored to adulthood by Eric the Red of the alien Shi'ar race, Magneto formed a new Brotherhood comprising Lifter, Burner, Shocker, Slither, and Peeper. When they failed to capture the mutant with two bodies known as Mister One and Mister Two, Magneto abandoned this team, though they remained together as the Mutant Force and later temporarily became the Resistants.
The mutant shapeshifter Mystique formed her own Brotherhood of Evil Mutants, recruiting Blob, Pyro, Avalanche, Destiny, and her own foster daughter, Rogue. Mystique sent the Brotherhood against Carol Danvers, then known as Ms. Marvel (later Binary and Warbird), which ultimately led to Rogue absorbing and retaining Danvers' powers and memories. Mystique intended for the Brotherhood to assassinate then-anti-mutant Senator Kelly, but they met defeat after the X-Men intervened and were incarcerated. Rogue freed the imprisoned members from captivity, but the male members were quickly recaptured after a struggle with the Galadorian Spaceknight named Rom. Mystique then sought to recruit the Dire Wraith/human half-breed Hybrid as a member; however, he proved too powerful for her to control, and the "Sisterhood" eventually aided Rom in temporarily destroying Hybrid. Subsequent efforts to target the X-Man Angel led to an encounter with Alison Blaire, the Dazzler, with whom Rogue quickly developed a fierce rivalry until Dazzler definitively defeated her.
Rogue eventually left the Brotherhood to seek help with controlling her powers and joined the X-Men. Soon after, Mystique's Brotherhood gained the support of the United States government by apprehending Magneto and became the first government-sponsored mutant team, Freedom Force. The team's ranks swelled with the addition of vigilantes Crimson Commando, Super Sabre, and Stonewall, as well as the interdimensional Spiral and Julia Carpenter, the new Spider-Woman. Freedom Force conducted various missions for the government, ultimately losing both Destiny and Stonewall in battle against the cyborg Reavers on Muir Island. After Mystique, Spiral, and Spider-Woman left the team, the remaining members were sent on a mission to rescue nuclear physicist Reinhold Kurtzmann from captivity in Kuwait. The operation went awry after they encountered the Arab super team Desert Sword. During the battle, Pyro killed both Kurtzman and Desert Sword operative Veil, Super Sabre was beheaded by Aminedi, and Crimson Commando was critically injured. Avalanche and Commando managed to escape alongside a squad of American soldiers, leaving Blob and Pyro to be captured.
Eventually the Toad sought to form a new Brotherhood, recruiting Blob, Pyro, Sauron, and Phantazia, and allied with the Morlocks to take down the mutant strike team X-Force. During the battle, both Sauron and the Morlocks' leader Masque were seemingly killed; however both later resurfaced, with Sauron rejoining the Brotherhood prior to a failed attack on X-Factor. Following a clash with the crime-fighting Darkhawk and the enigmatic Sleepwalker over the interdimensional mutant Portal, Toad's Brotherhood disbanded.
Soon after, X-Factor's then-leader Havok sought to expose the Clan Destine genetic experiments of the alternate reality Dark Beast. He created the impression that he had decided Xavier's dream was futile and re-formed the Brotherhood as a proactive mutant team against humanity, abandoning the "evil mutants" tag. With the telepathic Ever, Havok faked an assassination attempt on Daily Bugle publisher J. Jonah Jameson which was stopped by the X-Men. Havok then recruited the Dark Beast and his assassin Fatale into the Brotherhood in order to keep closer watch on the Dark Beast's activities, as well as Nate Grey. After Havok's true motives were revealed and the Dark Beast was defeated, Havok disbanded the Brotherhood and returned to X-Factor.
The next incarnation of the team came when Professor Xavier was imprisoned by the government-sanctioned Operation: Zero Tolerance. Freed by a new Brotherhood of Mutants led by the Blob and consisting of Toad, Post and Mimic, Xavier agreed to train them to better their chances of survival against the then-sentient computer Cerebro. After Cerebro was defeated by Xavier, the Brotherhood was employed by Mystique to recover the remains of X-51, the Machine Man, after which she reorganized the team. Mystique recruited some of her old teammates along with Sabretooth, Toad, Post, and Mastermind (Martinique Jason) with a view to launching another assassination attempt on then-presidential candidate Senator Kelly. As Mystique, Sabretooth and Toad created a diversion by attacking the Muir Island Research Facility, Post, Blob, Avalanche, and Mastermind targeted Kelly. In response, the X-Men split into two groups to stop the Brotherhood but were unable to prevent the destruction of Muir. They would have been too late to save Kelly if not for the timely arrival of former Brotherhood member Pyro, who was in the final stages of the deadly mutant-killing Legacy Virus and sought to redeem himself before he died. Pyro sacrificed his life to incinerate Post, thus preventing Kelly's death. Despite this selfless act, Kelly was ultimately killed by an anti-mutant protester who believed him to be a race traitor.
Following Mystique's imprisonment, many of the Brotherhood members were recruited by former X-Man Banshee into the paramilitary X-Corps group, leaving the way clear for a terrorist coalition to claim the name of The Brotherhood. Formed by mutant activists Hoffman and Marshal, this militant group engaged in worldwide terrorist activities before Marshal ultimately quit over Hoffman's growing hunger for power. Marshal became a government agent intent on taking Hoffman down and managed to convince three captured Brotherhood members to sell Hoffman out in exchange for their freedom. Ultimately, this Brotherhood was dismantled after many of its members, including Hoffman, were killed during a failed assassination attempt on Doop of the celebrity mutant group X-Force.
After infiltrating Xavier's school in the guise of the mutant healer Xorn, a Magneto imposter adopted the Institute's special class of students - Basilisk, Ernst, Martha Johansson, Beak, and Angel - as his Brotherhood. Joined by Toad and Esme of the Stepford Cuckoos, the faux Magneto attempted a hostile takeover of Manhattan. However, his inability to control the resulting chaos resulted in the fracturing of the Brotherhood after he inadvertently killed Basilisk and was himself decapitated by Wolverine.
Brotherhood was reorganized by Magneto's former Acolyte Exodus, who recruited Black Tom, Avalanche, Sabretooth, Mammomax, and Nocturne for an all-out attack on the X-Men. The Brotherhood planned their attack based on inside knowledge provided by an apparent turncoat X-Man, the Juggernaut; however, he was revealed to be a mole planted by the X-Men. After a pitched battle, Exodus' Brotherhood was defeated when the X-Man Xorn created a black hole from the microscopic star in his brain which pulled them in and closed behind them.
Recently, the Brotherhood was apparently reformed by the New Mutants: Cannonball, Magma, Moonstar and Sunspot, however, it was a ruse created by Donald Pierce, disguised as Cyclops.