A shipping vessel, the Genyu Maru II, is caught in a powerful typhoon that causes it to be shipwrecked on the presumed irradiated isle of Infant Island. A search party finds four of the sailors alive as they are sent to be treated for radiation sickness. Journalist Zenichiro "Snapping Turtle" Fukuda and his photographer Michi Hanamura infiltrate the examination. Miraculously, none of the survivors are contaminated with radiation, which they attribute to the juice provided to them by island natives. The news of natives present on Infant Island surprises the Rolisican government, which presumed the island uninhabited when they conducted hydrogen bomb tests on it. In response, the Rolisican Embassy co-sponsors a joint Japanese-Rolisican expedition to the island. On the expedition are radiation specialist Dr. Harada and linguist Shinichi Chujo, who is reluctantly interviewed by Fukuda and Michi. Prior to the expedition leaving, the journalists spot a shady Rolisican businessman named Clark Nelson. As the voyage is underway, Harada discusses with Chujo over Nelson's controlling attitude. In his room, Nelson discovers Fukuda as a stowaway.The expedition ship arrives on Infant Island as a team treks through a seemingly desolate and barren landscape. As they head further inland, they are surprised to find an oasis among the barren island. The expedition moves deeper into the jungle as Chujo encounters bizarre mold and is ensnared by a large carnivorous plant. As he struggles, he spots two tiny twin women before he's rescued and sent to the ship to recover. Fukuda talks with Chujo, who nicknames the minuscule women as the Small Beauties, or "Shobijin". The expedition resumes as the rest of the team encounters the Shobijin, small fairies who communicate through song. Nelson attempts to capture them before the rest of the Infant Island natives arrive to drive the expedition away. Fukuda arrives back in Japan as he and Chujo explore Nelson's past, discovering his prior attempts to exploit native women from the Amazon. Chujo then shows Fukuda an inscription he found on Infant Island which repeats a symbol that says, "Mothra". Meanwhile, Nelson has return to Infant Island where he finds and abducts the fairies. As the natives arrive, Nelson and his team proceed to shoot them down and escape. An injured native arrives to a shrine and prays to their mythical deity, Mothra.Fukuda discovers Nelson has captured the Shobijin and coerced them to preform in front of audiences for his "Secret Fairies Show". Fukuda and Chujo attend as the fairies sing, praying to their god Mothra. Chujo attempts to get Nelson to release the fairies, but Nelson refuses by citing that the fairies are not human, but merely merchandise. Chujo and the journalist manage to meet the captive fairies, who reveal their ability to speak via telepathy. They reveal that Mothra will come to rescue them, but they are worried that innocent people might suffer as she arrives. Back on Infant Island, the natives gather in prayer as Mothra hatches from an enormous egg, revealing a giant larvae.Fukuda's newspaper begins to accused Nelson of holding the women against their will as Nelson threatens to file a libel suit against the paper. Fukuda warns Nelson that Mothra will come to the fairies' rescue, but Nelson ignores this warning as he continues to exploit the twins for profit. As this occurs, the larvae begins to swim across the Pacific Ocean while accusations from the press start to mount on Nelson, who continues to ignore any responsibility. Chujo heads off to talk to the fairies as Fukuda deals with Nelson's goons. The fairies reveal they are unable to stop Mothra's arrival in Japan, with Chujo attempting to block their telepathic waves with a synthetic material. Mothra continues her voyage as she is attack by the JSDF. The Rolisican government backs Nelson's claims as he assumes Mothra will be destroyed.Nelson soon discovers his show to be canceled as Mothra is revealed to be alive and attacks a dam on the Japanese mainland. The public and Rolisican government turn on Nelson as he starts to flee with the fairies to Rolisica. Mothra makes her way to Tokyo, undeterred by the Self Defense Force's counterattacks. The larvae crawls onto Tokyo Tower and proceeds to cocoon itself as Nelson boards incognito on a plane to Rolisica. The Rolisican government provides aid to Japan as they attempt to destroy Mothra with Atomic Heat Ray Guns, which Fukuda and Michi observe from a safe distance. Back in Rolisica, Nelson overhears that the Mothra cocoon has been incinerated and is pleased to hear of what he presumes to be the monster's demise.However, Mothra emerges from the cocoon in her imago form as Chujo realizes that she is flying towards Rolisica. Nelson is frustrated to hear Mothra has survived and annihilated the Rolisican Air Force. He attempts to flee with the fairies as Fukuda, Chujo, and Michi board a plane to Rolisica to catch Him and return the fairies to Infant Island. Mothra soon arrives to the Rolisican capital of New Kirk City as Nelson refuses to capitulate. Nelson is soon confronted by the citizens of Rolisica as he attempts one last escape before he is killed in a shootout with police. Chujo and the journalists soon arrive as they liberate the fairies. Chujo observes the religious significance of Mothra's symbol, which resembles the Christian cross.Chujo realizes that the symbol can be used to attract Mothra and has it painted on an airport runway. Church bells ring as Mothra stops her rampage and arrives on the airport tarmac. Fukuda, Chujo, and Michi approach Mothra and liberate the Shobijin. The twin fairies thank them for their kindness as they are promised that Infant Island will be left in peace. The fairies join Mothra, who takes flight as everyone bids her farewell. Mothra soon arrives on Infand Island as the meaning of the inscription is revealed, A prayer for peace and prosperity to last for all eternity.