- Xavier Mansion. Upon entry, the X-Men discover that the mansion is in ruins. Enemies in this stage simply attack, although the red-colored enemies are more aggressive. Upon defeating Blob, the team discovers that the mansion was in ruins, and that the X-Men within this dimension have fled to Department H to avoid the Sentinels.
- Canadian Showdown. Introduces green suited enemies, which have a slow-moving projectile attack. This stage is simply a short walk to the underground base, guarded by Cable.
- Department H. Upon entering the base, they are greeted by an unknown enemy who states that they are trespassing on Apocalypse's grounds. There is mention of Weapon Omega and Alpha flight, neither of which appear in-game. The mid-boss of this stage is Sabertooth, and the end-boss is Gambit. The team discovers that there is a warp gate in this dimension. As a step to reach the gate, they need to take out the communication's grid, also home to a sentinel base.
- Blackbird. In this stage, Phoenix attacks the Blackbird with a group of enemies. She has a powerful attack that makes melee ineffective.
- Sentinel Base. The Sentinels are assisted by Juggernaut, and the X-Men need to take out the cooling system. Once done, they will need to find the gate, and will speak with Forge.
- Undersea Base. The red enemies have a ranged attack, and crouch when doing them. They are immune to attacks during this. After defeating Magneto, the X-Men make contact with Genesis. He gives instructions on how to locate and destroy the gate.
- Paris. Midboss is Nightcrawler, and Psylocke is found at the end. After going through Paris, they learn the location of the warp gate is at the Golden Gate ridge in San Francisco.
- The Savage Land. In order to draw attention away from the gate, the X-Men need to destroy a geothermal tap supplying power. Sauron and Beast serve as the bosses for this stage.
- Statue of Liberty. The X-Men need to further distrupt communications by taking out the satellite dish. Colossus is the end-stage boss, and defeating him finishes the stage regardless of other enemies on-screen.
- Genosha. The X-Men perform further damage by taking out the cloning facility. Boss is the Silver Samauri.
- The Golden Gate. After clearing out the enemies, the X-Men proceed through the warp gate. The gate is defeanted by Angel and Bishop.
- Blue Area of the Moon. The previous warp gate only operates towards the moon. To return home, the X-Men need to fight through Pyro and Apocalypse, destroy and enter the main gate.
Of these characters, the only significant difference is attack types. Cyclops and Storm have a projectile attack available, while Wolverine and Rogue will charge forward when given the same command. All characters have more basic melee attacks.
At the end of each stage, the player is given a number of points to distribute among the mutant power, vitality, or strength. Unallocated points are lost forever.
The game itself is not too much different than most other beat 'em ups, although there is a significant dissonance between some attacks and their hitboxes. For example, what would obviously be a ground based attack may appear to hit targets that are already in the air.
Static memory locations:
- $02000D84: Character health
- $02000CD4: Time remaining
- $02000DF0: "Rage" meter
- $020103D8: Bonus points for skill improvement, during skill improvement screen.