SpaceGodzilla emerges when Godzilla's cells, sent into space by Biollante in 1990 and by Mothra in 1993, are exposed to the intense radiation of a black hole. This radiation births an extraterrestrial threat that heads toward Earth and quickly makes its presence felt, even destroying a NASA space station along the way.
On Baas Island, the UNGCC—led by Koji Shinjo and Kiyoshi Sato—arrives to plant a mind-control device on Godzilla, hoping to bend the mighty monster to their authority. Meanwhile, the Cosmos, Mothra's twin priestesses, appear to psychic Miki Saegusa and warn her of the looming menace. The JSDF responds with M.O.G.U.E.R.A., a mobile force meant to stand in for Mechagodzilla, but the new extraterrestrial threat proves formidable, inflicting damage as it moves.
SpaceGodzilla lands on Baas Island and attacks Little Godzilla, forcing Godzilla to intervene. The elder monster finds himself overwhelmed and unable to stop SpaceGodzilla from trapping Little Godzilla in a crystal prison. With the threat now en route to Japan, SpaceGodzilla follows, while Godzilla chases after in pursuit.
In the meantime, Miki is abducted by yakuza who want to harness her psychic abilities to control Godzilla. She is eventually rescued by Shinjo, Sato, and Akira Yuki, just as SpaceGodzilla lands in central Fukuoka and constructs a massive fortress from celestial crystals. The situation escalates as SpaceGodzilla intensifies its grip, and the M.O.G.U.E.R.A., now piloted by Shinjo, Sato, and Yuki, engages the creature but faces a seemingly overwhelming power.
Godzilla himself arrives in Kagoshima Bay to confront SpaceGodzilla, yet the extraterrestrial foe maintains the upper hand. The JSDF uncovers a crucial weakness: SpaceGodzilla is siphoning energy through Fukuoka Tower, converting Earth’s core to fuel its assault and threaten the planet’s volcanic stability. The battle intensifies as M.O.G.U.E.R.A. splits into two units—the Star Falcon, commanded by Yuki, and the Land M.O.G.U.E.R.A., a tank piloted by Shinjo and Sato. These units strike the crystal fortress, while Godzilla delivers a decisive push that topples Fukuoka Tower and severs SpaceGodzilla’s energy supply.
M.O.G.U.E.R.A. rapidly reforms and begins dismantling SpaceGodzilla’s crystal shoulder formations, weakening the invader. SpaceGodzilla retaliates, injuring M.O.G.U.E.R.A., but is ultimately incinerated by Godzilla’s supercharged atomic breath. With SpaceGodzilla defeated, the UNGCC warns that continued pollution of Earth’s orbit could invite another such threat someday.
As Godzilla returns toward Baas Island, Miki uses her psychic powers to lift the mind-control device from Godzilla’s neck. The grateful creature nods to her in thanks. Back on Baas Island, Little Godzilla is freed from the crystal prison and resumes his playful, atomic bubble-blowing antics, signaling a fragile moment of reclaimed peace.
