In a world where a small percentage of the population are mutants with superhuman abilities, society is divided on how to deal with them. Some, like the telepathic Professor Charles Xavier, believe in peaceful coexistence and have established a school for young mutants to learn to control their powers and use them for the benefit of humanity. Others, such as the Holocaust survivor and powerful mutant Magneto, see no hope for mutual acceptance and aim to conquer humanity for mutantkind's survival.

During a mission to rescue a mutant from an aggressive situation, Xavier's team of X-Men encounter Logan, a loner with a forgotten past and an ability to heal rapidly, and Rogue, a young girl whose touch drains life and powers from others. As Rogue and Logan seek sanctuary within Xavier's School for Gifted Youngsters, Magneto plans to use Rogue's powers to further his agenda. This sets the stage for a clash of ideologies, with the safety of the world hanging in the balance as the X-Men strive to stop Magneto’s potentially devastating scheme.