The past, showing what formed Magneto's hatred and ruthlessness. We see his parents being herded into a concentration camp with others. When separated, his powers manifest. A steel gate is bent, until he is knocked unconscious by a gun. His parents and many others become victims of the Nazi's unrelenting bigotry. So he knows firsthand how vile the human heart can be.
Senator Kelly wants a vote on the mutant registration act. He's like a modern day McCarthy. People who have done nothing but be born with powers are to register as mutants. That will make it easier for him to point his witch-hunting bigots toward them and let things happen. If they refuse to be registered, they should be locked away.
Rogue is a young girl whose powers manifest. If she touches someone, she steals their life force. If it's a mutant, she steals their powers. She has no control over her powers, so she runs away. She's in Canada when she meets Wolverine. He's also a mutant, and very gruff. But he gives her a ride. Then a tree falls in front of his truck. He's thrown out, but heals immediately. She's trapped in the burning truck. He's attacked by Sabretooth and unable to help her. Storm and Cyclops show up and rescue them. They're taken to Professor Xavier's School for Gifted Students.
The Professor enrolls Rogue and explains things to Wolverine. He tells Wolvie that the school is for mutants, where they can learn to control their powers and be among others who accept them.
Mystique kidnaps Senator Kelly and takes him to Magneto. They use a machine to change his genetic structure and turn him into a mutant. That way he'll be on their side, just like the others they plan to use the machine on. Kelly escapes and goes to Xavier's, fearing hospitals now that he's different.
Rogue hears Wolverine having an nightmare. She tries to wake him, but he stabs her with his claws. She touches him to steal his healing ability to save herself. Then one of her peers tells her no one wants her there anymore. They're afraid of her. The first rule is to not use one's powers on others. She runs away.
Wolverine goes after her. But so does Magneto. The 'peer' who told her to leave was Mystique, trying to get her away from safety. Mystique also messed with Cerebro, the machine Xavier could use to find Rogue. Instead, it puts him in a coma.
Jean uses Cerebro to find Rogue. That's when they realize what Magneto is really up to. What he plans to do with her will most likely kill the child as well as hundreds of people. The team suits up and heads off the the big battle.