A nuclear waste dump, located on an island in the South Seas, is contaminating the nearby land. This is causing abnormal mutations to affect local vegetation, animals and insect life. The company responsible also starts to clear-cut the land, turning the once lush terrain into a barren wasteland. When a typhoon strikes the island, a large landslide unearths a mammoth egg that falls into the ocean and drifts off toward 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 the giant egg's origin. Among the research teams is a man by the name of Murakami, who by chance stumbles upon 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; furthermore, she 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 such a disaster.

Meanwhile in Japan, before Murakami has time to warn the authorities, the egg hatches. A larval Mothra emerges from the shell, along with another unrecognizable creature. This second monster is Gigamoth, a Mothra mutated beyond recognition as a result of the local radiation found on the island in the South Seas. After hatching, Gigamoth quickly flees from the scene.

In hopes to prevent further disaster, Murakami brings Mana to try and warn of the danger mankind is in. However, upon arriving Mana is struck with a surge of psychic energy as the tiny woman realizes that Godzilla is reacting to the nuclear fallout of Gigamoth. Shortly afterwards, a report comes in that the mutated insect has in fact engaged Godzilla near a nuclear power plant in the Kanto area.

Mana, in an attempt to fend off Godzilla, teleports herself inside Gigamoth's body, merging with the monster in order to control it. Mana then commands Gigamoth to emit an acidic mist that corrodes everything in the area as well as severally burning Godzilla's skin. Having the upper hand, Gigamoth webs up the injured Godzilla before shoving the King of the Monsters into the sea. The mutated Mothra then goes up to the nuclear power plant and encases itself in a cocoon, as to draw energy from the power plant while it transforms. At this point Mana severs the link between them, just as the Self Defense Force mobilizes a new squad of masers, capable of firing rays that freeze their target. The masers unleash shot after shot at the cocoon, but the plan proves ineffective as Gigamoth emerges from a sheath of frost in its adult form. However, the creature was not given sufficient time to complete its metamorphosis, and as a result its wings have not fully matured, making flight impossible. This set back does not stop the creature from converging on Tokyo, though. Meanwhile, in the sea outside of the power plant, Godzilla's wounds have healed, as the creature breaks free of the webbing that encased it.

Later, Godzilla, after emerging from the sea, confronts Gigamoth for the second time in Atami. The King of the Monsters fires his atomic ray at Gigamoth, but the mutated insect is unfazed by the ray; in fact, the creature's body sparks as the mutant Mothra absorbs the nuclear energy and its wings fully mature. Gigamoth then takes off into the sky, leaving behind Godzilla.

After witnessing the battle, Murakami realizes that Gigamoth must have formed from an extreme exposure to radiation. He 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, though, and merges Murakami with Mothra, while simultaneously merging herself with Gigamoth. This fails, however, as Mothra refuses to respond to any of Murakami commands and the two unmerge with the giant monsters. Murakami goes back to work, finishing the antibody bacteria; however, he also comes to terms with himself and realizes that he is falling in love with Mana.

Meanwhile, in the Fuji area, Gigamoth lays several giant eggs of its own. Shortly afterwards, Godzilla appears, attracted by the Gigamoth's radioactivity, and prepares to engage the giant insect once more. However, before the creatures can fight, a fleet of jets appear overhead and unload a payload of rockets containing Murakami's recently finished antibody bacteria. Godzilla is unfazed by the rockets, but Gigamoth is left weakened and very vulnerable by the bacteria as Godzilla converges on his weakened prey. Suddenly, Mothra arrives in her imago form and having merged with Mana. The giant moth lets loose a wave of poisonous pollen that paralyzes Godzilla, but not before he lets off a blast of his atomic ray that strikes Mothra and sends the kaiju plummeting out of the sky. Mothra spies the weakened Gigamoth below and the two siblings make eye contact as Mothra shifts it course and spears itself onto Gigamoth's horn. Blood from Mothra begins to pour out of the creature, drenching Gigamoth and its eggs, causing both to dissolve. It's Mana's hope that Mothra's body contains a small amount of mutant bacteria and that the two insects might combine to form a creature that is immune to the effects of Murakami's antibody bacteria. The plan works, as the two are engulfed by a glowing light, from which emerges Mothra's true form.

Mana, after severing her link with the giant moth, appears before 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 comforts him by telling him he will meet someone like her very soon. Mana then merges with Mothra again and proceeds to cocoon Godzilla. The giant insect then grabs the cocoon and dives into the sea, taking Godzilla with it.

Shortly afterwards a search of the ocean is conducted but neither creature is found and both are presumed dead.

Months later, Murakami returns to the South Seas' island where he first met Mana, hoping that by some chance to find her again. While standing on the beach, he sees a woman emerge from the ocean who looks just like Mana. He approaches her to find out that she is a research oceanographer. The two fall in love as Mana's prediction proves true.

After Mothra vs. Bagan had long been canceled and Godzilla vs. King Ghidorah (1991) was wrapping up production, work began on Godzilla vs. Gigamoth, sometimes referred to as Mothra vs. Gigamoth.

Koichi Kawakita and Minoru Yoshida wrote the early script for the film and submitted it in 1991. Toho wasn't satisfied with the treatment, though, and the project was eventually scrapped. The company tried other attempts, dead set on creating a film pitting Godzilla and Mothra against each other. The next draft, written by Wataru Mimura, retitled the project Godzilla vs. Mothra and was submitted that same year in 1991. This too was scrapped as Godzilla vs. Biollante (1989) writer Kazuki Omori was brought in, creating Godzilla vs. Mothra from his Mothra vs. Bagan script before finally adding in the Battra character in a later draft and ending up with the final product: Godzilla vs. Mothra (1992). In the end, this concept contributed very little to the final movie beyond Gigamoth being a similar idea to Battra.

In terms of the Godzilla vs. Gigamoth concept, several questions do arise. The foremost being why Mana didn't stop Murakami from completing his bacteria, especially since she was willing to sacrifice Mothra to stop the effect? It should also be mentioned that the DAG-MB96, although not with that name of course, were originally going to appear in this project before later appearing in Godzilla vs. Destoroyah (1995).

Note: No picture of Gigamoth exists beyond concept art drawings. The above conception of him was done through Toho Kingdom's interpretation of the concept drawing.