Godzilla cells brought into space by Biollante and Mothra are exposed to intense radiation from a black hole, resulting in the birth of "SpaceGodzilla", which quickly makes its way to Earth, destroying a NASA space station along the way.
Meanwhile, members of the United Nations Godzilla Countermeasures Center arrive at Birth Island in order to plant a mind control device on Godzilla. The Cosmos, Mothra's twin priestesses, appear to psychic Miki Saegusa and warn her of SpaceGodzilla's arrival. M.O.G.U.E.R.A., a mecha built by the JSDF to replace Mechagodzilla, is sent in to intercept SpaceGodzilla, but suffers damage in the process.
SpaceGodzilla lands on Birth Island and attacks Godzilla's son, Little Godzilla. Godzilla intervenes but finds itself overwhelmed by SpaceGodzilla, and is powerless to stop its clone from trapping Little Godzilla in a crystal prison. SpaceGodzilla leaves for Japan with Godzilla in pursuit.
Shortly thereafter, the Yakuza abduct Miki and bring her back to their base in Fukuoka in an attempt to use her psychic abilities to gain control over Godzilla. Miki is saved by a rescue team before SpaceGodzilla arrives. 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 in Kagoshima Bay and fights SpaceGodzilla, but SpaceGodzilla easily gains 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 it. SpaceGodzilla critically damages M.O.G.U.E.R.A., but is subsequently incinerated by Godzilla's supercharged atomic ray.
Godzilla makes its way back to Birth Island after Miki uses her psychic powers to remove the mind control device from its neck. Little Godzilla is then free from the crystal prison and begins blowing radioactive bubbles.