To demonstrate the superiority of mutants to mankind, Magneto uses his power of magnetism to cause another rocket to crash at sea. The next day, he threatens to Cape Citadel by force. Then he goes to the base to prove that ordinary weapons are useless against him and to claim the military compound in the name of homo superior. Magneto is soon confronted by the X-Men, a team of young mutants who combine their skills to dodge his attacks and chase the villain away from the base.

Magneto has assembled the Brotherhood of Evil Mutants composed of Mastermind and the Toad to achieve his plans to rule the Earth. The Scarlet Witch and her brother Quicksilver have also joined the team when Wanda became in debt with the master of magnetism who saved her from the superstitious inhabitants of a small European village. Magneto commandeers a freighter and attacks the small Republic of San Marco. Mastermind uses his powers to instill fear among its inhabitants so they can control them and soon, Magneto has built a real army. The X-Men arrive and invade his hew castle. Pietro is appalled by Magneto's decision to sacrifice the population of San Marco to destroy the X-Men with a large bomb. When the heroes are about to defeat them, Magneto flees with the rest of his team.

Magneto sends his Brotherhood on a search for the X-Men. Investigating magnetic disturbances in New-York, Thor finds Magneto's submersible fortress and battles him. After an attack by the Evil Mutants, the X-Men track down Magneto to his fort, forcing him to abandon the camouflaged lair while Thor destroys it.

The Brotherhood of Evil Mutants once more engage in battle against the X-Men who force them to escape from their space station.

Gambling on the hypothesis that he might be a mutant and the knowledge that he wants to dominate the surface world, Magneto offers Namor an alliance. But when the Sea Prince sees how Magneto treats the Scarlet Witch, he chooses not to ally himself with him. After he has destroyed Magneto's amplifier, the Evil Mutants are forced to escape from the X-Men.

Looking for a way to defeat the X-Men, Magneto finds the Blob in a circus but the carnies get into a fight with his Brotherhood of Evil Mutants. The Blob refuses to join Magneto until a concussion brings his memory of the X-Men back. During a fight against the X-Men, the fat mutant realizes that Magneto was willing to sacrifice him to destroy his enemy so he quits the team.

Magneto offers the Stranger to join his brotherhood, but the X-Men interfere and engage in a battle during which the powerful alien offers him to join him instead. While Magneto insists that he is the master, the Stranger wraps him and the Toad in cocoons and takes them back to his home world as mutant specimens.

In the aftermath of the X-Men's battle with the Sentinels, Magneto has sneaked into their headquarters in their absence, and one by one, he manages to capture all of them except for Iceman who lies in critical condition in a hospital. Then he locks them all into a hot air balloon and sends them up to suffocate in orbit. Taking control of the school, Magneto gets a visit from Warren Worthington's parents and puts them under his magnetic control. Since they gave birth to a mutant, he plans to use their genetics to create an army of mutant slaves. Probing Magneto's mind, Professor X learns that he escaped the Stranger's prison planet by repairing a seemingly useless ship, leaving the Toad behind. Meanwhile, Iceman has left the hospital and has put a stop to Magneto's mutant-creating machine. As he battles Iceman, the other X-Men join in. The fight ends when the Stranger, informed of Magneto's escape by the professor, arrives on Earth to take the villain back to his prison planet.