Thousands of years ago, Mechagodzilla, a robotic monster, was driven into the sea by Godzilla, Earth's defender. Recently, a submarine was dispatched to locate Mechagodzilla's remains. Overpowered by humans from the Third Planet, the scholar Dr. Mafune is forced to control two monsters through experiments and inventions in order to conquer Earth. However, when Mechagodzilla is ordered to destroy a ship, a fierce battle ensues.