In the year 2026, a corrupt mutant group called "Scumocide" plots to control the universe from Metro City. The hero, Captain Commando, assembles a team of three renegades: Ginzu the Ninja, Baby Head, and Mack the Knife, to help him foil Scumocide's plans.
The player chooses one of these four characters and must fight their way through an army of genetically engineered super-criminal, traveling through various locations such as a bank, museum, circus, aquarium, and more, until reaching the planet "Callisto", where the evil behind "Scumocide" awaits. Each character has unique special attacks: Captain Commando can use his suit's power to shoot electricity, Baby Head rides a mech suit that does more damage, and Mack uses short knives. The game ends with each location defeated by a boss before proceeding to the next one.