In ancient times, a monster know as Bagan stalked the country of China. The beast was referred to as a living god, a yamato, and protected the small inhabitants of the forest from which he dwelled. Eventually, as years drag on, the yamato becomes sealed in large body of ice; however, it was documented, in a centuries-old collection of Chinese poetry, that the return of the "primordial dragon" will occur when "evil rulers despoil the land." Prophecy becomes reality when global warming begins to ravage the earth in modern times.

In the Himalayas, Bagan's ancient, glacial tomb cracks open and melts away. The beast lives once more, his mission is clear: to destroy those who have ravaged the Earth, to destroy mankind. Even as the living god is freed from his tomb, in Borneo a mammoth egg is discovered. Not long after being uncovered, a object appears in the sky: Mothra, an ancient monster of peace left behind by an alien civilization to safeguard the world from Bagan. The egg soon hatches there after, revealing it to be the egg of Mothra as a larva crawls out.

The monsters then embark on a series of worldwide battles, as Mothra and her kin venture to Bagan's current location. The first confrontation occurs in Singapore, as the Mothras are unable to stop the yamato. The creatures continue their skirmish in Bangkok; however, this time Bagan ends up killing the adult Mothra. With the tides of battle left to the offspring, the larvae Mothra builds a cocoon and changes into its Imago form. The final battle then follows, as Mothra and Bagan face off in Bangladesh for the final time. Despite the fact that Bagan has become even more powerful since their last confrontation, sprouting two giant wings to fly about, the beast is finally dispelled by Mothra and the world left in peace.

Following production of Godzilla's 17th outing, Toho set out to return their second most popular character, Mothra, to the big screen. For this project, Toho intended to pit Mothra against Bagan, a heavily revamped version of what was first conceived in The Return of Godzilla (1st Draft). The movie was also going to take place on a more global scale, with segments occurring in Thailand, Nepal, China, Malaysia and Indonesia. The screenplay was finished on April 4th, 1990 and the attached staff included: Kazuki Omori as writer/director, Koichi Kawakita as special effects director with Tomoyuki Tanaka and Shogo Tomiyama as producers.

Unfortunately, Godzilla vs. Biollante (1989) didn't meet the firm's expectations at the box office, and Mothra vs. Bagan was canceled as the company deemed it too risky to do a monster film without Godzilla. In the project's wake, and to commemorate their 60th anniversary as a company, Toho began working on Godzilla vs. King Ghidorah (1991) instead.

Out of all the unused projects, Mothra vs. Bagan is especially noteworthy for getting the furthest in development, even garnering the approval of producer Tanaka, before finally getting axed. Another interesting thing to note is that this movie was also planned to be the first reoccurring appearance of the Miki Saegusa character from Godzilla vs. Biollante (1989), and would have been her only role outside of the Godzilla films.

Many elements of the project would later be used in Rebirth of Mothra (1996).