News reporter Ichiro Sakai and photographer Junko Nakanishi take pictures of wreckage caused by a typhoon. They uncover a strange, bluish-gray object in the debris, not knowing its significance. Later that day, a giant egg is discovered on the shore. The local villagers salvage it and Kumayama, entrepreneur of Happy Enterprises buys the egg from the local villagers. Instead of letting scientists study the egg, Kumayama intends to exploit it. While Sakai, Junko, and Professor Miura are discussing the egg at a hotel, they spot Kumayama checking in. Kumayama meets with Jiro Torahata, the head of Happy Enterprises. They are unexpectedly confronted by tiny twin girls known as the Shobijin and try to capture them. The Shobijin escape and meet with Sakai, Nakanishi and Miura. They explain that the egg belongs to Mothra. If the egg hatches, the larva will cause great damage looking for food.

The trio agree to help and attempt to reason with Kumayama and Torahata but fail to do so and the Shobijin leave. Miura informs Sakai and Junko that the strange object they discovered is radioactive and return to the beach to find the source. Godzilla surfaces from buried mud and attacks Nagoya. Sakai, Junko, and Miura travel to Infant Island to request the Shobijin to send Mothra to defeat Godzilla. The natives and the Shobijin initially refuse due to the atrocities inflicted on the island and its inhabitants by nuclear testing, but are eventually convinced. However, the Shobijin warn them that Mothra is too old and nearing death.

Kumayama confronts Torahata and demands to get back the money that Torahata had recently swindled from him. Kumayama is shot by Torahata, then he too is killed when Godzilla destroys his hotel. Godzilla advances on the giant egg but is interrupted by Mothra. Mothra initially gains the upper-hand but is defeated by Godzilla’s atomic breath, and dies of exhaustion. The JSDF launch multiple attacks on Godzilla until two giant larvae hatch from Mothra’s egg. They follow Godzilla to Iwa Island, trap it with their silk spray and force Godzilla into the sea. Sakai, Junko, and Miura thank the Mothra larvae and Shobijin as they return to Infant Island.