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 extra lives in the form of collecting three "X" icons hidden throughout each stage.