Professor Xavier and his Uncanny X-Men are all that stand in the way of the rampage of Magneto and his henchmen. The X-Men: Wolverine, Cyclops, Storm, Colossus, Iceman and Nightcrawler, are ready to fight Magneto.

The Uncanny X-Men is an over-head view action game. Players begin by choosing two X-Men from the roster (the second either controlled by another player or the computer) and select one of five levels including a practice level. The goal in each level is to reach the hidden 'command center' and destroy it. The X-Men all share similar abilities, being able to move in any direction, jump and attack. Half of the characters (Storm, Iceman, Cyclops) have long range attacks while the other half (Wolverine, Nightcrawler, Colossus) must get in close range to punch the enemies. Each X-men can only sustain a certain number of hits before being defeated. Should the two X-Men both fall in battle, players will be able to choose two more to attempt the level again until all of the X-Men are used up.

Power-ups include an "S" which stops time, invincibility for a short time and a health restore. There is also a Magnet (symbol of Magneto) power-down which renders the X-men immobile for a short time.