The player controls military forces trying to prevent Godzilla and other giant monsters from destroying cities, including special vehicles such as the Super X2 and SY-3 from Destroy All Monsters. This game, released in place of an earlier announced game meant to star Rodan, was received poorly by audiences, due in part to a lack of a genuine plot, and due to the game having an extremely complex style of combat, which was difficult for many players to understand. It was the third Godzilla game for a Nintendo system to be released in North America, after Godzilla: Monster of Monsters for the Nintendo Entertainment System, and Godzilla for Nintendo Game Boy.
It would be followed by Super Godzilla for the Super Nintendo Entertainment System in 1993.
Japan is being ravaged by bizarre and powerful giant monsters. A reptilian creature called Baragon is creating earthquakes in an oil refinery, a high-speed pterosaur named Rodan is leaving sonic booms in his wake, a hideous blob of slime called Hedorah is feeding off of the city's toxic waste and growing larger every second, a giant caterpillar named Mothra is laying eggs in different parts of town, a giant octopus is destroying fishing ships in the harbor and devouring their crews, a terrible three-headed hydra named King Ghidorah is bringing fire to the skies, and Godzilla is plowing through everything around him. To make matters worse, a fleet of alien saucers has begun an invasion. Only the Japan Self-Defense Forces can stop them.
- Godzilla: The titular and most common monster, and one of the most powerful. If Godzilla seeks out an H-Bomb, he will end the game.
- Baragon: A tunneling creature, special ability is to dig underground and become invisible, but he can be detected by a radar car.
- Rodan: A flying, highly mobile monster. Rodan can heal if he is over a volcano. Also, he will be weak if he's on the ground.
- Hedorah: A monster made of polluted slime. In water he is invincible and almost always, heal.
- King Ghidorah: Three-headed space dragon, possibly the most powerful monster ever.
- Mothra: The moth monster, also appears in larva form. Initially an enemy, but in later missions becomes a friendly unit if the player finds its egg.
- UFO: A UFO. Fires beams that can initially be reflected with the Super X2's laser, but in later missions is so powerful that it punches right through.