After Yota is lost at sea, his brother Ryota steals a yacht with his two friends and a bank robber. However, the crew runs afoul of Ebirah, a giant lobster-like creature, and washes ashore on Letchi Island. There the Red Bamboo, a terrorist organization, manufactures heavy water for selling weapons of mass destruction and a yellow liquid that keeps Ebirah at bay, presumably controlling him. The Red Bamboo has enslaved natives from nearby Infant Island to create the yellow liquid, while the natives hope that Mothra will awaken in her winged, adult form and rescue them.
In their efforts to avoid capture, Ryota and his friends, aided by Daiyo, a native girl, come across Godzilla, who previously fought Ghidorah and is now sleeping within a cliffside cavern. The group devises a plan to defeat the Red Bamboo and escape the island. In the process, they awaken Godzilla using a makeshift lightning rod. Godzilla fights Ebirah, but the huge crustacean escapes. Godzilla is then attacked by a giant condor and a squadron of Red Bamboo fighter jets. Using his atomic ray, Godzilla destroys the jets and kills the giant bird.
The humans retrieve the missing Yata and free the enslaved natives as Godzilla begins to destroy the Red Bamboo’s base of operations, smashing a tower that causes a countdown that will destroy the island in a nuclear explosion. Godzilla fights Ebirah and defeats him, ripping his claws off, forcing him to retreat into the sea. The natives await for Mothra to carry them off in a large net. However, when she gets to the island, Mothra is challenged by Godzilla due to a previous confrontation. Mothra manages to repel Godzilla and save her people and the human heroes. Godzilla also escapes just before the bomb detonates and destroys the island.