The Acolytes are a group of mutants who have embraced the teachings of the mutant Magneto. Led originally by Fabian Cortez, the Acolytes first encountered Magneto on Asteroid M, a space station created by Magneto orbiting Earth. The Acolytes requested and were granted sanctuary by Magneto from American soldiers that were chasing them, and remained on Asteroid M.

The Acolytes first encountered the mutant team known as the X-Men when the Acolytes attempted to deliver retribution to the island nation of Genosha, which had recently granted freedom to its mutant slaves. The X-Men were defeated by the Acolytes and Magneto, and were taken to Asteroid M.

Soon after, Magneto kidnapped Professor Xavier and Dr. Moira MacTaggert, taking them to Asteroid M. An attempt to turn the captured X-Men was thwarted by the remaining X-Men, who had stormed Asteroid M in order to rescue their comrades. It was soon discovered that Cortez had betrayed Magneto, who had been injured by Wolverine. Cortez' "healing" had been causing further harm to Magneto, and the former Soviet Union had sent a pulse cannon to destroy Asteroid M and everyone aboard. Cortez escaped the destruction, as well as the X-Men. Magneto, however, remained on Asteroid M with the Acolytes Chrome, Annemarie, and Delgado. Asteroid M crashed in the Middle East upon reentry to Earth. During the reentry, Chrome used his power to change elements to protect Magneto from dying, but the Acolytes perished in the process. Magneto survived reentry, and disappeared for some time.

Cortez was revealed to be a member of the Upstarts, a group of young mutants vying for their own leadership by killing mutants for "points." Now that Magneto, believed to be dead, was elevated to the status of martyr (by Cortez' own hand), Cortez was able to recruit more mutants to the Acolytes' cause.

The next move by the Acolytes came about as the Acolytes Unuscione, Cargill (formerly Frenzy of the Alliance of Evil), and the Klienstock triplets attacked the Our Mother of the Sacred Heart School in upstate New York. The purpose of the attack was to capture a young boy who would become a mutant upon adolescence. The attack was stopped by the X-Men, and the boy was rescued after he was discarded by the Acolytes when he was discovered to have Down's Syndrome.

At some point during this time, Magneto, bitter after Cortez' betrayal, found and recruited the mutant known as Exodus. Magneto returned to space and created Avalon, a second space station created from Shi'ar technology that was stolen during the time that Magneto was in charge of Xavier's School for Gifted Youngsters.

After the attack on the Mother of the Sacred Heart School, the X-Men discovered the Acolytes were hidden in an abandoned monastery named Mont Saint Francis on the coast of France, where the Acolytes had taken the again-captured Dr. MacTaggert. MacTaggert was rescued, and the Acolytes were driven from the island.

The Acolytes then attacked a hospital in Wantaugh, Virginia, killing humans that were already dying. The government mutant team X-Factor was called in to investigate and while doing so captured the Acolyte Spoor. Spoor only revealed the Acolytes' plans in the presence of Quicksilver, who is Magneto's son. Spoor revealed that the Acolytes' next target was the military base in Camp Hayden, Kentucky. X-Factor journeyed to Camp Hayden and drove off the Acolytes, only to discover that Camp Hayden was actually a front for a plant producing the robotic Sentinels.

After the attack on Camp Hayden, Magneto returned with Exodus, revealed Cortez' betrayal, and wrested control of the Acolytes from him. To recruit other mutants, Magneto sent Exodus to retrieve the remaining New Mutants (Cannonball, Sunspot, Meltdown (then Boomer), and Rictor), along with the brainwashed former Mutant Liberation Front members, Rusty and Skids. Magneto reversed the brainwashing technique used on Rusty and Skids, who joined the Acolytes. The others refused, and escaped Avalon with the remaining members of X-Force, who followed them to the space station.

Magneto returned to Earth during the funeral of Illyana Rasputin, a young mutant who had recently died of the Legacy Virus. Magneto offered the assembled mutants at the funeral membership in the Acolytes, and the offer was accepted by Colossus, Illyana's brother, who had lost his belief in Xavier's dream. Colossus returned to Avalon and the X-Men soon assaulted the base. The attack ended when Professor Xavier wiped Magneto's mind clean, reducing him to a vegetative state. Exodus assumed leadership of the Acolytes, and remained on Avalon.

Cortez resurfaced in an attempt to take control of Genosha, taking Magneto's granddaughter Luna as a hostage. Luna was rescued by a combined effort of the X-Men, which included her father Quicksilver, and the Avengers, which included her mother, the Inhuman known as Crystal. Exodus killed Cortez during the rescue in the sewers beneath Hammer Bay, the capital city of Genosha.

The Acolytes remained on Avalon until they had retrieved a cocoon from space, which happened to house the dimensionally displaced mutant known as Holocaust. On Avalon, Holocaust reawakened, killed the Acolytes Rusty and Milan, and the ensuing fight between him and Exodus destroyed Avalon, plunging the Acolytes, along with the X-Men Cyclops and Phoenix, to Earth. Phoenix had landed safely, but Cyclops, along with the Acolytes Unuscione, Cargill, Scanner, and the remaining Klienstock twins, landed in the Australian Outback, where Cyclops led them to the former X-Men base in Australia, and the Acolytes were arrested.