Factor Three was a team of evil mutants fought and defeated by Professor X and the original X-Men. This is the Joint Venture Universe version of the organization.
Factor Six was the first terrorist organization comprised entirely of mutants, a precursor to the Brotherhood of Mutant Liberation. Indeed, most of its members would go on to be founding members of the latter organization.
As the name implies, Factor Six was comprised of six members. Each member of Factor Six (save Banshee, the last person to join) was contacted by a mysterious being known only as The Mutant Master, and enlisted with promises of greater power and their fondest wish granted:
- Jason Wyngarde, the illusionist known as Mastermind, was promised wealth and genuine power, as opposed to the illusory power he wielded already.
- Carmela Unuscione was promised revenge on the murderers of her father, who had died when he lost control of his powers while fighting an angry mob.
- Kevin Sydney, the shapeshifter Morph, was promised a cure to an unstable element within his mutation that was slowly killing him.
- Frederick J. Dukes, a strongman whose powers earned him nothing but scorn, derision, and cruelty from others, was saved from the brink of suicide and took the name "Stonewall" in honor of his grandfather, after being promised the opportunity to avenge himself on those who had wronged him.
- Porter Telford, the teleporter known as Vanisher, was simply offered a grand sum of money.
- Finally, Banshee, the last 'recruit', was forcibly captured by his younger brother, Black Tom Cassidy, and sold to Factor Six as an unwilling operative.
The enigmatic being known only as "The Mutant Master" existed only as a voice in the minds of the mutants whom he would recruit. He assembled Factor Six through telepathic contact and coordination, giving them missions and objectives without ever appearing to them in person.
The only people aware of the Mutant Master, outside of the organization itself, were Black Tom Cassidy, who had been contacted but not recruited by the mysterious being, and Professor Charles Xavier, who had detected a malevolent presence but been unable to pinpoint its specifics before he and his friend and ally Magneto could finish building the mutant-detecting computer known as Cerebro.
Indeed, it was Xavier and Magneto who first confronted Factor Six, attacking a federal government building in New York. This battle made the public aware of mutants, not only mutant threats like Factor Six, but of mutants with a desire to protect humanity and foster peace, like Xavier and Magneto himself.
After a number of battles with Xavier and Magneto that ended in a stalemate, the Mutant Master finally ordered Factor Six to murder the entire populace of Salem Center, New York, where he was certain Xavier and Magneto were based, though he did not know exactly where, as Xavier had not yet opened his Institute for Higher Learning.
These orders split Factor Six evenly between three factions. Unuscione and Mastermind were all too willing to comply with the order and slaughter humans, out of revenge in Unuscione's case and simple sadism in Masstermind's. Vanisher and Stonewall were uncertain -- they had signed on to make their lives easier, not to be responsible for the deaths of hundreds of innocents. And lastly, Morph had never wanted to hurt anyone in the first place, simply cure his condition and protect mutants from people who would hurt them. Banshee, of course, had never wanted to be part of the criminal organization in the first place, much less help them commit wholesale murder.
Eventually, this decision led to a fracturing of Factor Six during the final battle with Xavier and Magneto. Morph switched sides, and even helped Magneto free Banshee from the neural-interface costume that was overriding his control over his own body. Stonewall and Vanisher disappeared in the middle of the battle, Vanisher's teleporting powers effecting a tactical retreat to parts unknown. Finally, Mastermind and Unuscione were defeated by the combined forces, and carted off to a top-secret prison for superhumans founded in the aftermath of World War II.
The telepathic "Mutant Master" was not heard from again -- though some years later, when the X-Men were founded, another psychic mutant named Exodus would appear with a new team of mutant terrorists, the Brotherhood of Mutant Liberation, with some members being alumni of Factor Six. Whether the two teams are connected, or if Exodus could actually be the Mutant Master himself, is a subject of intense speculaiton on the part of both the X-Men and SHIELD.