Godzilla cells brought into space by Biollante and Mothra are exposed to intense radiation from a black hole. The celestial fission creates a highly aggressive extraterrestrial beast closely resembling Godzilla. This “SpaceGodzilla” quickly makes its way to Earth.
Meanwhile, a group of soldiers and scientists are setting up at Birth Island to try Project T against Godzilla, who has taken up residence on the isle. The plan is to plant a device on Godzilla which will allow the Japan Self Defense Forces to control the mutant dinosaur telepathically. With help from psychic Miki Saegusa, the project is put into action, but it ultimately fails. Afterward, the Cosmos, Mothra’s twin priestesses, appear to Miki and warn her of SpaceGodzilla’s arrival. With Mothra gone to space, the world will have to rely on Godzilla to stop the invader. SpaceGodzilla gets closer and closer to Earth, destroying a NASA space station along the way. M.O.G.U.E.R.A., a giant penguin-like robot built by the JSDF to replace the Mechagodzilla, is sent in to intercept SpaceGodzilla, but the alien uses a number of psychic attacks to cripple the robot, forcing it to retreat.
Attracted to Godzilla’s radiation, SpaceGodzilla lands on Birth Island, where it finds Godzilla’s son, Little Godzilla. SpaceGodzilla mercilessly attacks the small creature when he approaches it curiously, and Godzilla comes to his son’s rescue. Godzilla puts up a good fight, but finds himself overwhelmed by SpaceGodzilla’s power and is knocked out. With Godzilla temporarily subdued, SpaceGodzilla creates a small cage made of crystals and traps Little Godzilla inside of it. It then leaves for Japan, intending to destroy it. Godzilla, after failing to free his son from the cage, pursues SpaceGodzilla.
Shortly thereafter, the Yakuza capture Miki and brings her back to their base in Fukuoka in an attempt to use Project T to gain control of Godzilla. Fortunately, a recovery team is successfully dispatched and Miki and the team escape before SpaceGodzilla arrives and destroys the building. SpaceGodzilla lands in central Fukuoka and forms a massive fortress of celestial crystals. M.O.G.U.E.R.A. arrives to once again fight SpaceGodzilla, but is still no match for it. Godzilla arrives inKagoshima Bay and fights SpaceGodzilla, but SpaceGodzilla’s cosmic powers easily allow it to gain the upper hand.
The JSDF discovers that SpaceGodzilla is using Fukuoka Tower as a power converter, using it to transform the Earth’s core into an energy that SpaceGodzilla can absorb, slowly killing the planet. While Godzilla wrestles with SpaceGodzilla, M.O.G.U.E.R.A. splits into two different mechs: the Star Falcon, a flying battleship, and the Land Moguera, a tank. The mechs damage the crystal fortress while Godzilla pushes over Fukuoka Tower, cutting off SpaceGodzilla’s energy supply. M.O.G.U.E.R.A. quickly reforms and blasts off SpaceGodzilla’s crystal-like shoulder formations, weakening him. Enraged, SpaceGodzilla beats M.O.G.U.E.R.A. into submission and starts to throttle Godzilla, who further wounds SpaceGodzilla by gouging out his eyes.
With SpaceGodzilla brutally beaten and blinded, M.O.G.U.E.R.A. uses up the last of its power supply by ramming into the alien beast, but SpaceGodzilla impales M.O.G.U.E.R.A. with his tail and hurls it into the remains of the crystal fortress. Godzilla blasts SpaceGodzilla with his atomic ray, sending him crashing on top of M.O.G.U.E.R.A.’s remains. With a supercharged atomic blast, Godzilla finally eradicates SpaceGodzilla, and cosmic energy floats from the inferno and vanishes in the atmosphere.
Having won the fight, Godzilla makes his way back to Birth Island. Before he departs, Miki uses her psychic powers to remove the mind control device from Godzilla’s neck; he turns to her and nods in gratitude. Little Godzilla is then free from the crystal prison and can blow bubbles of fire.