Biollante and Mothra both entered space after their respective battles with Godzilla, and each brought G-Cells with them. Unfortunately, some of these Godzilla cells managed to enter a black hole, where they were exposed to the energy of an untold multitude of stars. The genetic material was altered, and a new beast was born. Its purpose was to dominate the planet Earth, and the only way it could accomplish this goal was by destroying its only obstacle: Godzilla.

The monster traveled through space at high speed and soon found itself contending with Moguera, humanity's weapon against monsters such as this. However, SpaceGodzilla easily withstood the force of Moguera's plasma laser cannons, and it countered with electromagnetic energy rings and a corona beam. The machine was sent into an uncontrollable spin, as Moguera turned out to be little in the way of a challenge whatsoever.

Born of a black hole, and having journeyed vast distances through the outer realms of the solar system, SpaceGodzilla had finally come to earth. The monstrosity landed on Birth Island, where he had sent energy-rich crystals ahead of him. Little Godzilla approached SpaceGodzilla cautiously, and he was viciously attacked. Godzilla appeared on the scene and fired his heat ray at SpaceGodzilla. The two monsters became locked in a beam battle as Little Godzilla turned to his father for safety. Godzilla shielded Little Godzilla from SpaceGodzilla's attacks, but the terrible tyrant used his telekinesis to entrap the young monster inside of one of his crystals. SpaceGodzilla took to the sky, and Godzilla could only watch in horror as it escaped. Godzilla pursued by sea.

SpaceGodzilla flew over Sapporo, Yamagata, and Nagashima, shorting and electromagnetically altering electronic equipment along the way. SpaceGodzilla finally landed in Fukuoka, where it instilled a well of cosmic energy into the nearby Fukuoka Tower. He built a crystal fortress around him, in order to draw energy whenever necessary. After he finished creating his bizarre stronghold, an enhanced Moguera suddenly arrived. Moguera fired its weaponry at SpaceGodzilla, and began to attack it at a short-range with its nose drill. SpaceGodzilla reacted by unleashing his corona beam, and Moguera started to pull back and fire its chest beam. SpaceGodzilla gathered more energy and sent Moguera crashing to the ground with another blast of arching energy from its mouth. It roared and fired another beam at Moguera, who quickly retreated.

Meanwhile, Godzilla finally breached the outer fringes of SpaceGodzilla's crystal fortress and started to march inward amongst the crystal towers. SpaceGodzilla fired his corona beam and the monsters clashed! SpaceGodzilla, with the help of the vast crystal reserve, dug deep into his array of powers and lifted Godzilla telekinetically with his Gravity Tornado, only to throw the nuclear menace into a tall building. The crystal towers started to rocket into the sky as SpaceGodzilla lifted himself with his telekinetic powers, ever firing his corona beam at Godzilla. Unfortunately, Godzilla's heat ray was frequently halted by a transparent crystal energy shield. Godzilla started to destroy the crystal towers, in order to sap SpaceGodzilla's power supply, but dozens of the crystals started to plummet to the ground, in an attempt to injure the Earth monster.

As the war raged on, Moguera separated into Star Falcon and Land Moguera. Star Falcon attacked SpaceGodzilla from the sky, as Land Moguera fired on Fukuoka Tower. Godzilla aided Land Moguera by toppling the damaged tower, and SpaceGodzilla lost its main energy source. The space monster began to suffer attacks from Godzilla, Star Falcon, and Land Moguera. The latter two merged again, and Moguera fired all of its weaponry at SpaceGodzilla. Godzilla, meanwhile, was attempting to bite the area where SpaceGodzilla gathered all of its energy. Moguera accidentally knocked Godzilla into a nearby building as it destroyed SpaceGodzilla's shoulder crystals, and, in the process, lost its left hand to the corona beam. SpaceGodzilla used its tail to throw Moguera aside, and Godzilla began to regain strength and rise again. Godzilla started to blast the weakened SpaceGodzilla with his heat ray as Moguera further injured the monster by crashing into it. Moguera was down for the count, as Godzilla continued to hit the extraterrestrial monster with his beam. SpaceGodzilla was pulsing with a red glow, and Godzilla finally finished off the dying monster with his spiral fire ray.

SpaceGodzilla exploded, and much like its supposed predecessor Biollante, its energy swirled into the sky, never to be seen again. SpaceGodzilla, that awful monster from space, was no more. Little Godzilla was freed from his crystal prison, and Godzilla began his long journey back to Birth Island, where he would once again reunite with his beloved son.