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 United Nations assembles the ultimate weapon to defeat Godzilla, while scientists discover a fresh pteranodon egg on a remote Japanese island.

The Earth is headed for disaster and when an archeological research team visits Infant Island to find out why, they discover two tiny women who reveal that the Earth is fighting back for all the harm humans have done here and sends out the evil Battra to destroy us. The Cosmos, as the girls are called, offer their help by calling Mothra to battle the creature. Unfortunately, Godzilla also appears and a three way battle begins that threatens to destroy Japan.