Godzilla cells brought into space by Biollante, in 1990,[b] and Mothra, in 1993,[c] 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 Earth's 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. (Mobile Operations G-Force Universal Expert Robot: Aero-type), 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 Little Godzilla with the Corona Beam. Godzilla intervenes but finds itself overwhelmed by SpaceGodzilla's other abilities, and is powerless to stop the 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 through Earth's volcanos. While Godzilla wrestles with SpaceGodzilla, M.O.G.U.E.R.A. splits into two different mechas: the Star Falcon, a flying battleship, and the Land M.O.G.U.E.R.A., a tank with a large drill in front of it. The mechas 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 then critically damages M.O.G.U.E.R.A. but is subsequently incinerated by Godzilla's supercharged atomic heat ray. SpaceGodzilla is destroyed, but the JSDF claims that if they keep polluting space another SpaceGodzilla may appear someday.

Godzilla makes its way back to Baas Island after Miki uses her psychic powers to remove the mind control device from its neck. Godzilla turns to her and nods in gratitude. Little Godzilla is then freed from the crystal prison and begins blowing tiny radioactive bubbles.