Hedorah, Kenpachirō Satsuma — an amorphous extraterrestrial from the Horsehead Nebula — is carried to Earth by a comet. On arrival, it feeds on Earth's pollutants and grows into a poisonous sea monster capable of producing sulfuric acid. After it sinks an oil tanker and attacks Dr. Toru Yano, Akira Yamanouchi the scientist, and his young son Ken Hiroyuki Kawase, the doctor is scarred and the threat is made public. Ken [Hiroyuki Kawase] has visions of Godzilla, Haruo Nakajima fighting the world's pollution and believes Godzilla will come to mankind's aid against Hedorah.
Hedorah mutates into an amphibious form, allowing it to move onto land to feed on more pollution. It heads toward a power station to consume the smoke from its chimneys, where it is confronted by Godzilla, Haruo Nakajima. Hedorah overpowers Godzilla and retreats into the ocean, but pieces of its body are flung off and crawl back into the sea to grow anew, setting the stage for an even stronger return. It comes back shortly afterward in a flying form, then assumes its full form, displaying some of its most formidable powers yet.
Thousands of people across Japan are killed by Hedorah's raids. As hope fades, a Mount Fuji party is held to celebrate one last day of life before the world succumbs to the alien threat. Ken [Hiroyuki Kawase], Yukio Keuchi [Toshio Shiba], Miki Fujiyama [Keiko Mari], and the other partygoers realize that Godzilla and Hedorah have converged on Mount Fuji for a decisive showdown. During the battle, Godzilla is quickly outmatched by Hedorah's durability and strength, suffering the loss of an eye and a deep chemical burn to a hand from contact with Hedorah's acidic body. Godzilla is nearly killed when Hedorah throws it into a pit and attempts to drown it in a deluge of chemical sludge.
Dr. Toru Yano and his wife Toshie [Toshie Kimura] have determined that drying out Hedorah's body may destroy the otherwise invincible monster. As the fight rages, the JSDF builds two gigantic electrodes and powers them up in a bid to give Godzilla a chance to break free and return to the fight. When the power briefly falters, Godzilla reactivates the devices with its atomic breath, dehydrating Hedorah's exterior. The alien's body splits open, and Hedorah, trying to escape in its flying form, is pursued by Godzilla's aerial assault, which uses its own atomic breath as a jet to close the gap. Godzilla drags the dried remains back to the electrodes and continues to dehydrate them until the creature disintegrates into dust. Godzilla returns to the sea, glowering at the surviving humans, and Ken bids farewell to Godzilla.
