The player takes control of five X-Men who each have their own objectives, and different moves and capabilities activated by certain control combinations. The player has a limited number of lives that count for all five X-Men and not one individually.
The levels may be played in any order. At the end of each level, a boss must be battled and defeated. The next three levels are linear and require each boss level to be defeated. This is followed by two straightforward boss battles in the Danger Room. Finally only one of the X-Men can be selected, each one going through a different end level.
After beating the first five stages, a password can be acquired. The game has health pickups,as well as the option to gain lives if collecting three “X” icons hidden throughout each stage.
Beast – Possesses superhuman physical strength, agility and ape-like appearance.
Cyclops – Produces powerful, uncontrollable beams of concussive force from his eyes, forcing him to wear specialized visor at all times.
Gambit – Has the ability to manipulate kinetic energy and charge objects with it and is also skilled in card-throwing, hand-to-hand and staff combat.
Psylocke – The only playable female character, Psylocke can use her telepathic powers to form a ‘psychic knife’ from her fist. An expert martial artist, she has the most techniques of all the playable characters.
Wolverine – A gruff mutant possessing superhuman senses, enhanced physical capabilities, adamantium coated bones and claws and regenerative abilities. The game however does not feature his healing factor.
Charles Xavier sends five of his X-Men to sabotage various operations and structures on the Genosha island complex to liberate mutants in captivity. Further investigation reveals Queen Brood and Tusk involved in this matter and headed by Apocalypse.
After defeating all evil forces on Genosha. Xavier finds out that Magneto intends to destroy Genosha from his space station Avalon. To prepare for the confrontation, Xavier tests the five X-Men in the Danger Room to defeat holograms of Omega Red and Juggernaut. After passing the tests, the X-Men go their separate paths inside Avalon facing and defeating Exodus and then battling Magneto and thwarting his plans.