After a fishing boat is attacked, the sole surviving crew member realizes it is none other than a resurrected Godzilla. However, efforts to bring the story to light are suppressed by the Japanese government amid growing political tensions between the United States and the Soviet Union, who are both willing to bomb Japan to stop the monster.

When Mothra went into outer space to stop a meteor from reaching Earth, she accidentally took with cells from Godzilla and remaining cells from Biollante that inhabited our atmosphere. The combined cells went through a black hole and created a new creature, Space Godzilla. Space Godzilla heads to Earth to confront Godzilla, Junior Godzilla, and the new G-Force robot, MOGERA.