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Young Magneto enters the concentration camp in Poland of 1944. His mother and his father were killed there. At the start of the comic, Magneto, is at the concentration camp where he was held and was reflecting on what happened there.
The mutant problem in the nation is growing; there is a fear of mutants. One mutant in Kansas resists arrest from police officers claiming that he just wants to be left alone and is shot to death.
Back in a time where Xavier and Magneto were good friends, they witnessed the murder of a young mutant girl just because she was a mutant. It angers Magneto and it fuels his rage that he has against humans and their hatred of mutants. Magneto believes that mutants are the next step in the evolutionary chain and that they will one day dominate the world. Xavier believes that mutants and humans will one day be able to live in peace with one another. Magneto has been through the Holocaust and does not desire to go through another one (humans killing mutants).
Xavier convinces Magneto to go back to America with him and create the Xavier Institute in Westchester County, New York. Magneto helps Xavier build Cerebro.
A Nazi Officer named Hans Von Shank (he was the one who ran the concentration camp that Magneto was in). Magneto was originally going to kill Hans himself, but he didn’t. It was because of Hans that the friendship between Xavier and Magneto fell apart. Hans was in custody in an American federal prison awaiting trial for crimes against humanity. Hans went to Israel before he came to America to hide from his crimes (he said that it was easier for him to hide where he was least suspected…among his enemies noses).
This comic explains Magneto's origin for the X-Men movie trilogy.