The microscopic alien life-form Hedorah feeds on Earth’s pollution and grows into a poisonous, acid-secreting sea monster. After he sinks an oil tanker and attacks Dr. Toru Yano and his young son Ken Yano, scarring the doctor, 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 amphibious form, allowing it to move onto land to feed on additional sources of pollution. Hedorah, having emerged at a power station to consume pollutant gases from the smokestacks, 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-like shape, then assuming its strongest form of all, its “Perfect Form”, which demonstrates some of the strongest powers it has access to yet.

Thousands of people die in Hedorah’s raids and even Godzilla is unable to defend against Hedorah’s poisonous emissions. As hope sinks, a party is thrown on Mt. Fuji to celebrate one last day of life before Japan – and then, the rest of the world – succumbs to Hedorah. Ken Yano, Yukio Keuchi, Miki Fujinomiya, and the other partygoers realize that Godzilla and Hedorah have come to Mt. Fuji as well for a decisive confrontation. During the battle, Godzilla fights valiantly against Hedorah, but is overpowered by the amorphous alien, losing an eye and having its hand burnt to the bone by Hedorah’s acidic body tissues, which corrodes anything it comes into contact with. Finally, Godzilla is almost killed by Hedorah after Hedorah hurls Godzilla into a pit, then proceeds to attempt to drown Godzilla in a deluge of chemical sludge.

Dr. Toru Yano and his wife Toshie Yano has determined that drying out Hedorah’s body may destroy the otherwise unkillable monster. While Godzilla and Hedorah fought, the JSDF swiftly constructed two gigantic electrodes for this purpose, and attempted to fire them, giving Godzilla the chance to return to the fight.

All of a sudden the electrodes short out, the power cut off by Godzilla and Hedorah’s violent battle. Godzilla reactivates and energises the electrodes with its atomic heat 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 heat ray to give chase. Godzilla drags Hedorah back to the electrodes and continues to dehydrate it until Hedorah is on the brink of defeat. Godzilla tears open Hedorah’s dried-out body and exposes it to the electrodes again, dehydrating the pieces until nothing remains but dust.

Godzilla returns to the sea, but not before pausing to gaze sternly at the surviving humans. Ken Yano bids goodbye to Godzilla.