A typhoon has battered the Kurta coastline and halted a land reclamation project. Journalist Ichiro Sakai and his photographer Junko Nakanishi arrive on the scene to report on the wreckage. The pair are soon called upon by their newspaper to head off to Shizunoura after an enormous egg is discovered on the shore and salvaged by the local fishermen.Sakai and Junko arrive and try to ask Professor Miura some questions while he attempts to inspect the egg. Miura's examination is soon halted by the arrival of Kumayama, an entrepreneur of a firm called Happy Enterprises. Kumayama explains that he bought the egg from the local villagers and plans to make it an attraction by charging admission. Sakai and Junko disagree with Kumayama, believing that he has no right to claim ownership of the egg.Later that night at a hotel, Sakai, Junko, and Miura are discussing their options when they discover Kumayama checking in. Sakai begins to suspect someone else is backing Kumayama and sets out to investigate. Kumayama walks into the room of Jiro Torahata and the two begin to discuss their plans to commercially exploit the egg by building a theme park around it as a tourist attraction. The pair are interrupted by the arrival of the Shobijin, Mothra's twin fairies, who plea with the entrepreneurs to return the egg to Mothra and the people of Infant Island. Kumayama and Torahata ignore their pleas and attempt to capture the fairies, only to be interrupted by Sakai. The Shobijin make their escape and introduce themselves to Sakai, Junko, and Miura outside the hotel. The fairies explain that the recent typhoon has washed Mothra's egg to Japan and wish for it to be returned returned before the larva hatches. They do not want the newborn larvae to cause unintentional damage as it searches for food and returns home to their Island. The trio agree to help as Mothra is revealed among the trees.They arrive to the construction site of the egg's incubator and confront Kumayama and Torahata. The pair scoff at their claims as Sakai attempts to convince them that the situation is a matter of trust. The Shobijin are revealed and make another plea for the egg's return. Kumayama then attempts to buy the fairies, causing Sakai and the others to leave in disgust. As they return to the hotel and deliberate their options, they notice the fairies have disappeared. Disheartened, the Shobijin have decided to return back to Infant Island with Mothra, thanking Sakai, Junko, and Miura for their kindness.Kumayama is later confronted by the fishermen for the money he owes from the egg's purchase and the land it's on. Promising their payment, Kumayama asks Torahata for a monetary loan. Torahata agrees, on the condition that Kumayama provides Mothra's egg as collateral. Kumayama reluctantly agrees.At the newspaper office, Sakai expresses doubt over his writing that doesn't appear to be swaying public opinion on the situation. Junko arrives to bring Sakai to the laboratory of Professor Miura. The pair are decontaminated and head out to Kurata beach. As they examine for radiation, Godzilla emerges from the ground and heads off toward the industrial area of Yokkaichi and the city of Nagoya.Sakai, Junko, and Miura return to their newspaper office where they discuss with the editor on how to stop the monster. Their fellow reporter Nakamura arrives and makes a suggestion that they could ask Mothra's help to defeat Godzilla. Sakai is skeptical of the idea and is hesitant to ask the people of Infant Island for help since they failed to return the egg to Mothra and her people. Realizing they have no other option, Sakai, Junko, and Miura decide to head off to Infant Island to make a plea of their own.As they arrive on the island, they are captured by natives and brought to the tribe's chief. The chief asks what their intentions are as the three reveal that they seek Mothra's help. The people of Infant Island refuse, expressing that they have lost their trust in the outside world. Their island home has been left desolate due to atomic testing and Mothra's egg has not been return. Dismayed, the trio hear the Shobijin singing a haunting melody and make their way towards them. Sakai, Junko, and Miura proceed to make their case to the Shobijin, but they too refuse to help, expressing that they have no faith in their world. Junko takes a stand and makes a plea to the Infant Islanders. She understands that while they may distrust them, innocent people are dying because of Godzilla. Regardless of who they are, people have a right to live and Japan needs their help. Sakai steps in, mentioning that they too wish to live in a world were people can trust and help one another. No matter how difficult it may seem they will never give up in attempting to make the world a better place. As the islanders contemplate their decision, Mothra herself makes the choice to help Japan. However, this will prove to be Mothra's final act as she is nearing her death and will be unable to return to the island.The JSDF reveals their plans against Godzilla as Sakai, Junko, and Miura return to the egg and find Nakamura waiting there. They inquire about Kumayama, who's revealed to have stormed off in rage. Having lost everything, Kumayama barges into Torahata's hotel room and demands Torahata returned all the money that was conned from him. As Torahata refuses, the two get into a fistfight where Kumayama beats Torahata down. Kumayama then makes his way to Torahata's money cabinet and begins to take as much as he can. Coming to his senses, Torahata notices Godzilla approaching the hotel and grabs a gun. As he kills Kumayama, Torahata attempts to escape with as much money as he can carry, only to be crushed to death when Godzilla destroys the hotel.Godzilla then proceeds towards the egg as the journalists watch from afar. Sakai expresses faith that Mothra will arrive as Godzilla destroys the incubator. Just as Godzilla is about to destroy the egg, Mothra arrives to confront him. The two monsters fight a fierce battle as Mothra manages to drag Godzilla away. However, Godzilla repeatedly fires his atomic ray at Mothra and severely burns her. The injured Mothra flies off and rests on top of her egg as Godzilla walks away. The Shobijin then explain that while Mothra may be dead, her legacy will continue through her children born from the egg.Meanwhile, the JSDF attempt to halt Godzilla by electrocuting the monster with artificial lightning. The first attempt has air and ground forces lead Godzilla towards the lightning generators. But the monster manages to destroy the generators as the JSDF regroups. Back at the egg, the Shobijin sing a prayer as Sakai, Junko, and Miura wait for it to hatch. The JSDF make a final attempt to stop Godzilla by covering the beast in conductive nets and attempting to electrocute the monster to death. They almost succeed before a generator fails and Godzilla manages to free himself.Mothra's egg finally hatches, revealing two twin larvae. Godzilla makes his way towards Iwa Island, where a school teacher and her students have become trapped. Learning of this, Sakai and the others head on a boat to rescue the children as the Mothra larvae make their way to the island. Unable to defeat Godzilla with strength, the Mothra larvae use their wits and proceed to wrap Godzilla up in silk. With Godzilla distracted, Sakai, Junko, Miura, and Nakamura find and rescue the teacher and her students. The larvae manage to fully cocoon Godzilla as he plunges into the ocean. With the Mothra larvae victorious, the group return the children and head off to bid the larvae farewell. As the larvae make their way back home, Nakamura inquires about thanking them. Sakai responds that the only way to thank them is to create a better world, based on mutual trust for their fellow human beings.