Magneto's experience in the Auschwitz concentration camp shapes his perspective on mutants and the rest of the world. Determined to avoid such atrocities against mutants, he is willing to do whatever it takes to protect his own. He has faith that mutants ("Higher Homo") will become the dominant way of life on the planet. However, he constantly hesitates between peaceful coexistence with homo sapiens, due to his tendency to reinforce his superiority over all humanity.

The first act of terrorism that Magneto carried out was an attack on a US military base in Cape Canaveral. Magneto is frustrated by the mutant students of Charles Xavier, the X Men.4 After forming the mutant Brotherhood, Magneto briefly conquers the fictitious South American nation of San Marco in the hope of establishing a mutant land there, but the X- Men stop him again.5 The Magneto Brotherhood was made up of the Toad, Master Mind and Magneto's own sons, Pietro and Wanda (now called Mercury and Scarlet Witch respectively). Apparently, Magneto knew of their existence and saved them from dying at the hands of a fearful mob. In gratitude, they agreed to join the Brotherhood, but at that time they ignored that Magneto was their father and he was their children.

After several unsuccessful attempts to unite more mutants to his cause, Magneto tries to force the loyalty of a powerful man who only says he is a "Stranger". The reality is that he is an extraterrestrial in a special mission that comes to an end when he goes to his home planet and takes Magneto (and Sapo) with him, where he remains for a long time. The Brotherhood of Magneto breaks down, and Mercury and the Scarlet Witch abandon him when they discover the truth. Finally Magneto manages to escape and return on his own to Earth, where he intends to reenlist everyone to his cause, but his plans are overshadowed by his former supporter, Sapo, who has grown tired of Magneto's mistreatment.

Using ancient and advanced alien technology found near the center of the Earth, Magneto creates an artificial humanoid which he calls "Alpha, the Maximum Mutant." But Alpha rebels against its creator and reduces Magneto to his childhood. Then Magneto is sent under the care of a former colleague of Charles Xavier, Dr. Moira MacTaggert, on Muir Island. There, MacTaggert vainly engages with the genetic code of the infant Magneto to prevent him from becoming "evil" when he reaches adulthood. However, genetic modifications lose their effects when Magneto reactivates his powers. Magneto is finally restored to adulthood when it is found on Muir Island by the alien agent of the Shi'Ar race named Erik the Red (an identity Cyclops had adopted years ago to infiltrate a base under Magneto's control)