As Space Godzilla approaches Earth, it creates a crystal fortress on a remote island in the Pacific Ocean. The fortress is powered by the psychic energy of a young girl named Miki Saegusa, who is able to communicate with Godzilla and other monsters.
Meanwhile, G-Force, the organization responsible for protecting the Earth from giant monsters, begins developing a new weapon called MOGERA. The robot is equipped with advanced weaponry and is designed to be the ultimate weapon against Space Godzilla.
When Godzilla and Junior Godzilla arrive on the island, they are attacked by Space Godzilla's crystal minions. The two monsters put up a fierce fight, but they are eventually overpowered.
The G-Force team then sends out MOGERA to confront Space Godzilla. The robot initially has the upper hand, but Space Godzilla proves to be a formidable opponent. MOGERA is eventually destroyed, and the G-Force team is left with no options.
As a last resort, Miki uses her psychic powers to reach out to Godzilla and convince him to combine his power with Junior Godzilla's. The two monsters merge into one, becoming a more powerful version of Godzilla known as Super Godzilla.
Super Godzilla engages in a final battle with Space Godzilla. The two monsters wage a destructive battle across the island until Super Godzilla is finally able to destroy the crystal fortress powering Space Godzilla. The resulting explosion kills Space Godzilla and sends Super Godzilla plummeting into the ocean.
The movie ends with Miki and G-Force wondering if Godzilla will ever return, while also hinting at the possibility of new monsters emerging to threaten the Earth once again.