The storyline of this game is set in the 1950s where a fleet of alien flying saucer warships invade the Earth, causing massive damage. The scientists of the world manage to create a series of secret weapons, which, when activated, let loose shock waves that short-circuit the saucers and cause them to crash. Unfortunately, each flying saucer is fueled by a green radioactive liquid, which leaks out from destroyed crafts. Through this and follow up effects, the fuel creates giant monsters and turns man made robots hostile as a result. The player acts as one of these monsters and battles against the rest, and himself in fictional cities across the globe and the remaining UFOs.

The story mode of the game starts out in Midtown Park where a giant gorilla called Congar defeats a wave of Military forces but is fought and defeated by the lead monster. In Gambler's Gulch, the lead monster also defeats the Godzilla styled beast, Togera. After Togera's defeat, a military class mech called Robo-47 and the military show up and attack the lead monster but are defeated as well. At a military base at Rosedale Canyon (similar to Roswell), the lead monster is confronted by giant ants and a Transformer style robot, Goliath Prime. Prime and the ants are all defeated. The military then decide to test their new weapon, Mecha-Congar, on the high speed mantis Preytor, who was attacking Metro City. Before they could fight the lead monster appears and defeats them both. The lead monster then travels to Century Airflield and defeats Raptros the dragon and his mate. Later when Atomic Island suffers from a meltdown, a pack of Kinecticlops appear and must be defeated, and then the lead monster must battle a large plant Biollante like creature called Vegon. Two Robo-47s stop a UFO attack in Baytown and try to slay the lead monster and fail. Even the combined might of Agamo and Magmo in Club Caldera fell to the lead monster. After defeating two Ultra-V robots at "Tsunopolis", the lead monster is abducted by an on-looking UFO that takes it back to the UFO mothership. There the lead monster has to fend off a few Aliens (three Zorgulons) before being abducted once more when the mothership explodes, causing the carrying UFO to crash into a Washington DC style Capital city. There, the alien leader Cerebulon attacks in a multi-layered battle suit like the Tripods from War of the Worlds. After Cerebulon is defeated, the lead monster victor watches as the last part of Cerebulon, a small timid insect like creature flees.