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.

The aftermath of the Oxygen Destroyer brings forth Destoroyah, a beast intent on killing Godzilla, who is on the verge of a nuclear meltdown.