The Alliance of Evil first appeared in X-Factor #5-6 (June–July 1986), and was created by writer Bob Layton and artist Jackson Guice. Two of its members, Tower and Frenzy, had appeared before the rest of the team.
The team subsequently appears in X-Factor #33 (October 1988), and New Mutants Annual #7 (1991).
The Alliance of Evil received an entry in the Official Handbook of the Marvel Universe Update '89 #1.
The Alliance of Evil was once Apocalypse's personal strike force, and carried out his bidding. Their first mission was to find and capture Michael Nowlan, a mutant with the ability to heighten other mutants' powers. When Nowlan tried to leave, they kidnapped his girlfriend, Suzy, to use as bait. X-Factor found Nowlan and vowed to protect him. When the Alliance traced him down, they threatened Suzy to make him power them up. The Alliance fought and defeated X-Factor, bringing Nowlan back to their master. X-Factor eventually found their hideout, and on Apocalypse's orders Nowlan powered up the Alliance again. When Suzy tried to escape, Stinger's bolts accidentally kill her. Nowlan killed himself, and Apocalypse abandoned the Alliance of Evil and escaped.
Much later, the Alliance of Evil caused a commotion over the Mutant Registration Act. X-Factor saw them on the news and immediately attacked the Alliance. They were defeated by X-Factor and taken into custody by Freedom Force.