In the first level, you control Spider-Man who must use his spider sense to disarm on
a several bombs located throughout an abandoned building. After you complete this level Spider-Man learns that the evil Arcade has kidnapped Storm, Cyclops, Wolverine, and Gambit. You must successfully complete each character's level (each set in Arcade's deadly funhouse) in order to get to control Spider-Man in a final battle with Arcade.
- Spider-Man's Levels: New York City rooftops with the bosses being Shocker, Rhino, Carnage, and the flying demon N'astirh.
- Storm's Levels: Underwater level with Storm having a limited air supply.
- Wolverine's Levels: Circus level with the bosses being Juggernaut and Apocalypse.
- Gambit's Levels: Two stages, both of which take place in a cave where a giant spiked ball is chasing you; the final boss is the Black Queen.
- Cyclops' Levels: Two stages, both of which take place in a Sentinel factory, with the final boss being the Master Mold.
The two 16-bit editions of the game were nearly identical, except the Sega edition removed the buzzing sound that occurred whenever Spider-Man's Spider-Sense occurred. The feature had existed in the Super Nintendo version.