An expedition to a remote isle by the name of Infant Island discovers a pygmy race of women living among the local natives. Called the Pichi Fairies, the small race piques the interest of some of the expedition members, who assault the natives with firearms and take away five of the fairies. Back in Japan, the 60 centimeter women become a national sensation as they are forced to participate in a series of concerts.

Meanwhile, a mammoth egg on Infant Island hatches to reveal a giant larva called Mothra. The creature ventures to Japan, destroying large parts of Tokyo on its way to the National Diet Building. Once there, Mothra encases itself in a giant cocoon on the side of the building, which eventually hatches to reveal her Imago form. With the creature airborne, the Self Defense Force finally swings into action by deploying a large squadron of jets. The two fractions clash, but Mothra proves victorious. Left unopposed, the giant moth begins to decimate the city until she finally comes across the Pichi Fairies. Landing, the creature picks up the fairies and flies off to return to Infant Island.

Based on the novel The Luminous Fairies and Mothra, this adaptation was penned by Shinichi Sekizawa, who submitted his first draft proposal in 1960. Vaguely titled The Giant Monster Thing, this early concept featured a race of tiny women alongside the movie's giant monster. A name for the fairies was not specified in this first proposal, as apparently even at this early stage Sekizawa was contemplating a name change from their original title of the Airenas from the book.

In an unusual turn of events, another draft proposal was submitted shortly after. Re-titled Giant Monster Mothra, this second proposal fleshed out the concept more, giving the small women the name of the "Pichi Fairies" while citing that five would be seen during the course of the film. The size of the Pichi Fairies was stated as being 60 centimeters, showing a strange level of detail in this respect for a draft proposal. For reference, that would have been roughly twice the size of the Shobijin. The idea was seen as a winner, as a more fleshed out screenplay was finally commissioned.

In 1960, the first script for the production was completed, and was accompanied by a storyboard to help relate the concept. The storyboard, infamous for showing a rather frightening interpretation of Mothra, displayed a number of different concepts compared to the final film, including Mothra squaring off with a squadron of jets and also building a cocoon on the Diet Building, a concept that would eventually return in Godzilla vs. Mothra (1992). A lot of this was about to change, though, with the signing of two popular singers to the project.

On January 14th, 1961, the second draft of Giant Monster Mothra was submitted. Since the first draft, the singing duet The Peanuts (Emi and Yumi Ito) had been attached to the production. Seeing a very lucrative idea in the making, the fairy role was altered to just that of the singing duo, while their name was also changed to the Shobijin. The concept would be altered even further by Sekizawa, as a third draft of the script was submitted on February 5th of that same year. Production on the movie was now in full swing, although the name Giant Monster Mothra hanged around for quite awhile, even being used on advance posters before it was shortened to simply Mothra (1961) for its final release.