The microscopic alien life-form Hedorah feeds on Earth's pollution and grows into a poisonous, acid-secreting sea monster. After it sinks an oil tanker and attacks Dr. Toru Yano and his young son Ken Yano, scarring them both, Hedorah's toxic existence is revealed to the public. Ken Yano has visions of Godzilla fighting the world's pollution, and insists Godzilla will come to humankind's aid against Hedorah.
Hedorah metamorphoses into an amphibian form, allowing it to move onto land to feed on additional sources of pollution. Hedorah is confronted by Godzilla. Hedorah is easily overpowered by Godzilla and retreats into the sea. During the fight, however, several pieces of its new body are flung nearby, which then crawl back into the sea to grow anew and allow the monster to become even more powerful. It returns shortly thereafter in a flying saucer shape demonstrating new, even deadlier forms which it can switch between at will.
Thousands of people die in Hedorah's raids and even Godzilla is overwhelmed by Hedorah's poisonous emissions. As hope sinks, a party is thrown on Mt. Fuji to celebrate one last day of life before humankind succumbs to Hedorah. Ken Yano, Yukio Keuchi, Miki Fujiyama, and the other party-goers realize that Godzilla and Hedorah have come to Mt. Fuji as well for a final confrontation.
Dr. Toru Yano and his wife Toshie Yano has determined that drying out Hedorah's body may destroy the otherwise unkillable monster. The JSDF swiftly constructs two gigantic electrodes for this purpose, but their power is cut off by Godzilla and Hedorah's violent battle. Godzilla energizes the electrodes with its atomic ray, dehydrating Hedorah's outer body. Hedorah sheds this outer body and takes flight to escape, but Godzilla propels itself through the air with its atomic ray to give chase. Godzilla drags Hedorah back to the electrodes and continues to dehydrate it until Hedorah dies. Godzilla tears apart Hedorah's dried-out body and dehydrates the pieces until nothing remains but dust.
With Ken Yano calling after him, Godzilla returns to the sea, but not before glaring threateningly at the surviving humanity whose pollution spawned Hedorah.