The Legacy Virus only afflicted the residents of Earth 42 for two days. However enough damage was done that many villains who were previously impervious to attack were now vulnerable. Magneto took advantage of this and gathered his Brotherhood. Together they began eliminating their rivals.
Magneto decided to form an alliance with Madelyne Pryor, the leader of the Sisterhood of Mutants. He pretended to help her team but in reality he was trying to destroy it. Magneto led the Sisterhood of Mutants into an ambush. His team would have destroyed the Sisterhood but unfortunately they were resilient. They fought back and the Brotherhood of Mutants was defeated. After the near destruction of her team, Madelyne Pryor decided to disband the Sisterhood of Mutants to ensure their safety from the Brotherhood of Mutants.
With the Sisterhood defeated, Magneto turned his attention towards one of his other rivals, Mister Sinister and his Marauders. Magneto and his Brotherhood attacked Sinister's lab, forcing him on the offensive and catching him completely off guard.
The battle lasted for quite some time. Magneto's team began to crumble before the Marauders but Magneto didn't let this stop him. He pressed on and eventually killed the Marauders however by this time; he had already lost most of the members of his team.
Magneto thought he had won but the fight was far from over. Marauder clones began pouring into the halls. Magneto and his team fought on. They took even more casualties because as they destroyed one clone, several more would take its place. Magneto pressed on alone and fought his way into the cloning chamber. He used his powers to crush the machine. Instantly the clones stopped coming and any existing clones slumped to the ground dead.
While Magneto shut down the cloning chamber, Mister Sinister killed the rest of his team. He spared Mystique after negotiating a deal with her. In exchange for her help in killing Magneto, he would give her any enhancement that she wanted. Mystique had no choice but to accept because if she didn't, Mister Sinister would kill her.
Together, Mister Sinister and Mystique ambushed Magneto. They were able to defeat him easily because he had become infected with the Legacy Virus. He lay on the ground slowly dying. Mister Sinister taunted his fallen foe but it was Magneto who got the final laugh. He used the last of his powers to destroy the lab in a massive explosion.