After his brother Yata is lost at sea, young Ryota steals a yacht with his two friends and a bank robber. This motley crew runs afoul of sea monster Ebirah, and washes up on the shore of Devil's Island, where a terrorist organization manufactures heavy water for their nefarious purposes, as well as a chemical that keeps Ebirah at bay. The organization, Red Bamboo, has enslaved natives from Infant Island to help them, but the natives hope to awaken a dormant Mothra to rescue them. In their efforts to avoid capture, Ryota and his friends, aided by a beautiful native girl, stumble across King Kong 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 King Kong using a lightning rod. King Kong fights Ebirah, but the giant shrimp escapes. King Kong 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 King Kong begins to destroy the base. King Kong smashes a tower that has a self destruct button that makes the island unstable. King Kong 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, King Kong challenges Mothra when she gets to the island. Mothra manages to push King Kong away and carry the people off. King Kong escapes the island just before it explodes.
Following the success of their animated series The King Kong Show co-produced with Toiei Animation, Rankin/Bass approached Toho with the rights to King Kong to produce a live-action film based on the show. Toho began production of Operation Robinson Crusoe: King Kong vs. Ebirah, but Rankin/Bass rejected the screenplay on the basis that it did not follow the show close enough. Rather than completely discard the screenplay, Toho replaced King Kong with Godzilla and slightly tweaked the film into Ebirah, Horror of the Deep. This explains why Godzilla displays uncharacteristic behavior in the film, such as drawing strength from electricity, his curiosity towards Daiyo, the usage of boulders to destroy the Red Bamboo Base, and his hostilities with Mothra (despite them now being allies as of Ghidorah, the Three-Headed Monster). Toho would eventually produce the film King Kong Escapes the next year, which followed the animated series much more closely.
- Due to this film being the precursor to Ebirah, Horror of the Deep, almost all the major elements of its plot can be seen in the final release.