Magneto appears in Wolverine and the X-Men voiced by Tom Kane in a rendition of Ian McKellen's portrayal of Magneto in the X-Men films. He is shown to rule the island of Genosha, where it appears most mutants are moving to, in light of recent anti-mutant feelings. Despite the government's treatment of mutants, they seem content to allow Magneto to promote Genosha in the United States with assorted poster and commercials. It is later revealed that Magneto found Professor X unconscious on Genosha after the destruction of the X-Mansion and took to caring for him. When the X-Men arrive to 'rescue him' Magneto turns over care to them, stating that they are his family. When Nightcrawler arrived in Genosha, he had his daughter Scarlet Witch give him a tour. During that time, he sends Mystique to the X-Mansion to "check up" on Professor X. Magneto, Scarlet Witch, and the Acolytes attacked Nightcrawler when he discovered Magneto's underground cells. When Nightcrawler did a lot of teleporting to warn the X-Men, Magneto had Mystique intercept him while he prepared a special cell for Nightcrawler. Magneto gave Quicksilver and his Brotherhood of Mutants a mission. During the transmission, Quicksilver tells his father that if they pull this off, he'd better receive a warm welcome back to Genosha. In "Battle Lines", Magneto had a talk with Senator Kelly about holding back the powerful mutants from being sent to Genosha. He later has his Acolytes raid the MRD prisons to free the mutants. In "Hunting Grounds", he finds out that Scarlet Witch and Nightcrawler had been abducted by Mojo. After the rescue, Scarlet Witch persuades Magneto to let Wolverine and Nightcrawler go. In "Backlash", Quicksilver was not pleased with Magneto when he cuts Quicksilver's Brotherhood of Mutants loose. After a chat with Quicksilver, he has Scarlet Witch notify the MRD of the Brotherhood's hideout. In "Aces and Eights", Senator Kelly sends Gambit to steal Magneto's helmet. When Gambit gets away without the helmet and Magneto learns of this, he was about to pummel Senator Kelly until intervention by the X-Men prevented this, showing Magneto and Kelly the true horror of the future their actions are creating.
While Kelly listens to reason and agrees to stop the Sentinel program, Magneto refuses to give up on his ambitions. In the three-part episode "Foresight", Magneto sends Mystique to pose as Senator Kelly to unleash the Sentinels on Genosha, making it appear as though Kelly started the attack. When the Sentinels attack Genosha, Magneto initially does nothing, claiming that the weak must be sacrificed so the strong can rally together. He then uses his powers to reprogram them to attack humans. He was knocked off his Sentinel by the Phoenix Force yet was rescued by Quicksilver who takes him back to Genosha. After the Phoenix Force was stopped, Scarlet Witch and Polaris had Blink teleport Magneto and Quicksilver away from Genosha. Finally seeing the currupt and misguided nature of her father, Scarlet Witch takes control of Genosho with the islanders' full support. Though Scarlet Witch tells Quicksilver that he's always welcome in Genosha, she also states that Genosha is no longer Magneto's country therefore banishing her own father.