Factor Three first appeared through two of its agents, Banshee and the Ogre. Oddly enough, though the organization's credo involved the prosperity of the mutant race by becoming the third World Power (after the US and then-Soviet USSR), The Ogre was not a mutant at all, but was merely a paid mercenary who relied on technology. Banshee, forced to submit to the Mutant Master's commands via a headpiece rigged to explode should he refuse, teamed up with The Ogre to kidnap Professor Charles Xavier. His fledgling X-Men thwarted their attempts, captured the Ogre, and freed Banshee.

Later, Factor Three freed the supervillain Juggernaut, serving to distract the X-Men while a second attempt was made to kidnap Professor X; this time they succeeded. With the help of Banshee, the X-Men were able to locate Factor Three's hidden base within the Alps, but were captured during the rescue attempt. Finally meeting the Mutant Master himself, along with his full array of henchmen, their plan was unveiled. They intended to cause nuclear war between the US and the Soviet Union, which would wipe out the human race.

The X-Men were able to escape the mountain base just before Mutant Master blew it up, and again thwarted their plans. Factor Three relocated to an alternate base, where Changeling, Mutant Master's second in command, discovered his plans to destroy mutantkind as well as humankind. Changeling freed Professor X and Banshee, who inadvertently destroyed the Mutant Master's cloaking device, revealing his alien appearance. The X-Men and the remainder of Factor Three joined forces in attacking Mutant Master, who committed suicide to avoid capture. With Mutant Master dead, Factor Three ceased to exist.