The game begins with the X-Men and Brotherhood of Mutants uniting forces to save Professor X and Polaris. Cyclops, Storm, and Wolverine meet up with Magneto, Mystique, and Sabretooth at a military prison outpost in Greenland to free Professor X. Upon freeing him, the teams relocate to the fictional mutant haven of Genosha. They find the island ravaged by Apocalypse's forces, and work through the wreckage and find out what he was searching for. They learn that Quicksilver was kidnapped by Apocalypse, who also kidnaps Beast from the X-Mansion. Beast manages to point the team in the direction of the Savage Land, a secret prehistoric preserve in Antarctica.