2,000 years ago, a giant monster named Bagan watched over ancient China. The kaiju rose to destroy threats to the Earth and protected the countryside. He was called a yamato, or living god, of the forest he dwelled in. Although the ancient people of China dispelled the creature, Chinese legends that were passed down through the ages claimed that the the return of the "primordial dragon" would occur "when evil rulers despoil the land."
This horrific prophecy becomes a nightmarish reality in the present day of 1990 when the glacier containing Bagan melts from rising global temperatures and the monster sets its sights of destroying mankind, now Earth's greatest threat. However, standing in Bagan's way is Mothra, a giant guardian moth left behind 12,000 years ago by an ancient but advanced civilization to defend humanity's existence. Mothra confronts Bagan in Singapore, but is soon beaten down by the creature due to her age. Some distance away, in Borneo, a gigantic egg begins to stir, and it soon hatches an infant Mothra, which crawls out to go help its mother. The three monsters then engage in a long battle in Bangkok. However, as the monsters' fight is ended, The larva is weakened. Just before the yamato has time to kill her offspring with his Plasma Energy Beam, the adult Mothra flies in the way of the blast, being killed unintentionally by Bagan.
After the adult Mothra sacrificed herself to save it, the larva quickly retreats to a remote island and spins a cocoon, while Bagan sprouts gigantic wings for flight back in Bangkok. The younger creature comes out of the cocoon, transforming into an adult Mothra. The two monsters then meet again, this time in Dhaka, Bangladesh, and fight for the final time. Bagan, though, has become even more powerful, thanks to his wings. However, Mothra discovers that Bagan's thirst for vengeance serves as his huge weakness, causing the battle to be turned to the deity's favor. The younger monster uses effective speed tactics, leaving the yamato panting. Luckily, after a long and brutal final battle, an exhausted Bagan is finally defeated by the younger Mothra and humanity is saved. Mothra flies away back to Borneo at sundown, and rests in peace.