In 1991, after Mothra vs. Bagan's cancellation, and with Godzilla vs. King Ghidorah's production coming to a close, Koichi Kawakita and Minoru Yoshida wrote the script for Godzilla vs. Gigamoth. The script did not seem satisfying to Toho so it was scrapped. Toho then became very interested in having a movie with Godzilla and Mothra, and so the project was retitled to Godzilla vs. Mothra and the next couple of scripts focused on Mothra fighting Godzilla. The first script after Gigamoth was written by Wataru Mimura and was submitted the same year, and was scrapped too. The second and final script, which became Godzilla vs. Mothra, was written by Kazuki Omori from his Mothra vs. Bagan script, with Battra added.
A nuclear waste dump on an island in the South Seas is contaminating the nearby land, causing abnormal mutations to affect local life. The company responsible also starts to deforestates the land and ruins its soil, turning the green terrain into a wasteland. When a typhoon strikes the island, a large landslide reveals a giant egg that falls into the ocean and drifts off towards Japan.
Shortly afterwards, word of the large egg approaching Japan starts flooding the media, and several research teams are sent to the island in the South Seas to investigate where the giant egg might have comef from. A man named Murakami is in one of the research teams, who finds a tiny woman living on the island, who isn't even a foot in height. The small woman introduces herself as Mana and explains that the giant egg belongs to Mothra. She also states that his country will be in great danger if the egg were to hatch near the main land. Murakami believes her story and agrees to help spread the word to avoid the a disaster.
Before Murakami has time to warn the authorities, the egg hatches into a larval Mothra and an unknown creature back in Japan. This second monster is Gigamoth, a heavily mutated Mothra mutated thanks to the radiation found on the island in the South Seas. After hatching, Gigamoth quickly flees.
Murakami brings Mana to try and warn of the danger mankind is in by the appearance of these two creatures, in hopes of preventing any disasters. However, when they arrive, Mana is struck with a surge of psychic energy as she realizes that Godzilla is reacting to the nuclear fallout of Gigamoth. Very soon, a report comes in that Gigamoth has in fact started to fight Godzilla near a nuclear power plant near Kanto.
Mana teleports herself inside Gigamoth's body and merges with it, with a plan to drive Godzilla away. Mana commands Gigamoth to fire an acidic mist, which corrodes everything in the area and burns Godzilla's skin. Gigamoth then webs up Godzilla and pushes him out into the sea. Gigamoth then goes up to the nuclear power plant and encases itself in a cocoon, seemingly trying to obtain energy from the power plant while it transforms. After Gigamoth does this, Mana stops controlling it, right when the Self Defense Force mobilizes a new squad of maser cannons. The masers fire many freezing beams at the cocoon, but the plan fails as Gigamoth comes out of the cocoon in its adult form. However, Gigamoth was not given enough time to complete its metamorphosis, and so its wings have not fully matured, making it unable to fly, and it proceeds to go to Tokyo. Meanwhile, Godzilla's wounds have healed, and he escapes the webs that kept him underwater.
Later, Godzilla faces Gigamoth for the second time in Atami. He fires his atomic breath at Gigamoth, but it doesn't get damaged by the beam, but rather absorbs the nuclear energy, making its wings fully developed.
After witnessing the battle, Murakami realizes that Gigamoth must have formed from an extreme exposure to radiation, and believes that he could develop an antibody bacteria that could separate the radiation from the mutant bacteria in the cell structure and neutralize Gigamoth's powers. Mana interrupts Murakami's study and merges Murakami with Mothra, while merging herself with Gigamoth. However, Mothra refuses to respond to any of Murakami's commands and the two un-merge with the insect monsters. Murakami then finishes the antibody bacteria and realizes that he is falling in love with Mana.
Meanwhile, in the Fuji area, Gigamoth lays a few giant eggs of its own. Shortly afterwards, Godzilla appears, attracted by the Gigamoth's radioactivity, and prepares himself to fight Gigamoth again. Before the creatures can fight, a fleet of jets appear and unload tens of rockets which contain Murakami's recently finished antibody bacteria at the two kaiju. Godzilla is not affected by the rockets, but Gigamoth is weakened and made very vulnerable by the bacteria. Suddenly, Mothra arrives, in her Imago form and merged with Mana, ready to battle Godzilla. Mothra fires poisonous pollen that paralyzes Godzilla just as Godzilla fires his atomic breath and hits Mothra, sending her to the ground. Mothra and Gigamoth make eye contact, and Mothra goes right into Gigamoth's horn, making her bleed, which dissolves Gigamoth and its eggs. Mana hoped that Mothra contained a bit of mutated bacteria which would create a new creature which would be unaffected by Murakami's antibodies. Her plan works, as the two are covered by a bright light, from which Mothra's true form comes out of.
Mana stops controlling Mothra and appears in front of Murakami for the final time. Murakami uses this opportunity to confess his love for her and asks that she let them both join with Mothra. Mana refuses, but tells him he will meet someone like her soon. Mana then merges with Mothra again and proceeds to cocoon Godzilla. Mothra then grabs the cocoon and dives into the sea, taking Godzilla with her.
Shortly afterwards, a search of the ocean is conducted, at which neither monster is found and both are presumed dead.
Months later, Murakami returns to the South Seas' island where he first met Mana, hoping to find her again. While standing on the beach, he sees a woman surface from sea who looks just like Mana. He walks up to her to find out that she is a research oceanographer. The two fall in love, just as Mana predicted.