Godzilla vs. the Sea Monster aka Ebirah, Horror of the Deep begins with Yata (Toru Ibuki) being lost at sea. His brother Ryota (Toru Watanabe) steals a yacht with his two friends and a bank robber, the crew runs afoul of the giant lobster Ebirah, and washes up on the shore of an island, where a terrorist organization manufactures heavy water for their purposes, as well as a chemical that keeps Ebirah at bay. The organization, known as the Red Bamboo, has enslaved natives from Infant Island to help them, but the natives hope to awaken Mothra (now a full-grown moth metamorphosed from the larva that appeared in Ghidorah, the Three-Headed Monster) to rescue them.
In their efforts to avoid capture, Ryota and his friends, aided by a beautiful native girl, stumble across Godzilla sleeping within a cliffside cavern. The group devises a plan to defeat the Red Bamboo and escape from the island. In the process, they wake Godzilla using a lightning rod. Godzilla fights Ebirah, but the giant crustacean escapes. Godzilla is then attacked by a giant condor and a squadron of Red Bamboo fighter jets, but destroys them.
The humans retrieve the missing Yata, free the enslaved natives and Godzilla begins to destroy the base. Godzilla smashes a tower that has a self-destruct button that makes the island unstable. Godzilla fights Ebirah and defeats it, ripping off both Ebirah’s claws and causing it to retreat into the sea. The natives summon Mothra to save everyone, however, Godzilla challenges Mothra when she gets to the island. Mothra manages to push Godzilla away and carry the people off. Godzilla escapes the island just before it explodes.