A typhoon in the Caroline Islands blows the Japanese ship Kingumaru off course, into the area of a Rolisican atomic testing site. The ship hits a reef and the ship's crew is forced to abandon ship. Search teams have little hope of finding survivors, given the area they sank in, but they do find four men on the barren shore of Baru Island. The men are rescued and taken back to Japan. Everyone marvels that they show no signs of radiation sickness. They claim that this is due to an elixir natives on the island made them drink. This claim shocks the examining Dr. Haradawa. Tsinchan Fukuda and his photographer Michi Hanamura infiltrate the examination, achieving a scoop for their paper through their subterfuge. Tsinchan realizes that the island is supposed to be deserted. This forms his headline. Rolisican officials claim to have made certain that Baru was deserted before the atomic tests and promise to launch an investigation.
Tsinchan and Michi go to interview Dr. Chujo Nakazo, an authority on that region. Something of a recluse, Chujo refuses to allow his picture to be taken and only reluctantly grants an interview. He warms to Tsinchan when Bulldog helps his son Shinji recapture his escaped pet mouse. Chujo admits that he is going on the joint Rolisican-Japanese expedition to Baru Island.
The Rolisicans arrive, and Clark Nelson holds a press conference, denying reporters to accompany the expedition in order that it may be run more efficiently. Tsinchan formulates a plan. At the send-off for the expedition ship, he slips away from Michi's side as the ship prepares to set sail.
Now at sea, Dr. Haradawa and Chujo discuss Nelson's draconian edicts regarding the expedition's discoveries. Nelson discovers Tsinchan in his room disguised as a cabin boy. The Rolisican does not believe Bulldog's claims that he was only dusting. Menacing Tsinchan with a pistol, Nelson soon discovers that Tsinchan is a reporter. Before things can progress further, Chujo enters Nelson's room, telling the man that he will obey the orders of the Rolisican government but not those of Clark Nelson. Tsinchan departs with Chujo. That night, as the ship enters the test area, the expedition members check their protective equipment. Dr. Haradawa has saved Tsinchan from the brig and Bulldog has joined the expedition as a guard, promising to curb his reporter instincts.
The next day, Dr. Haradawa briefs the expedition about the features of their protective suits, especially a built-in alarm siren should any of the men get into trouble. The expedition then heads to Baru. Although the outer shores are barren, the interior is lush and fertile, filled with strange plants. The scientists begin making their tests. Chujo becomes separated from Tsinchan and enters a cave filled with such bizarre plants that they can only be atomic mutations. One of these plants attacks Chujo and he sounds his alarm. Before he passes out, he sees two tiny women heading toward him.
Drawn by the siren, the rest of the expedition finds Chujo lying unconscious outside the cave. Chujo revives back on the ship, telling the others about the vampire plant and the tiny women who saved him. Chujo insists the tiny women were real. Smelling a story, Tsinchan begins to question Chujo, but the man goes to sleep. The next day, back on the island, an alarm again sounds. The entire expedition runs to the scene, angry to discover that it is Chujo trying to draw the twin fairies to him again. Chujo insists that he knows what he is doing.
Soon, however, Chujo does indeed find the fairies. All the men marvel at the tiny women, who speak to them excitedly in a Polynesian dialect only Chujo understands. They are distressed by the atomic bomb tests, a position that everyone can sympathize with. As the girls start to leave, Nelson has one of his henchmen capture them. The villain can see the fairies' importance, and his gun silences all protest from Tsinchan and the others. At that point, natives arrive, surrounding the expedition, clashing stones together menacingly. Although Nelson has no problem with inciting a massacre, the others are not so ruthless and lower their rifles. Nelson grudgingly tells his henchman to release the fairies. Both fairies and natives retreat back into the jungle while the expedition heads back to the ship.
The expedition returns to Japan with much fanfare. Tsinchan is reprimanded by Michi for not sending a single story back. Chujo investigates Nelson's past with Tsinchan, who holds that the man reminds him of some sort of crooked international art dealer. He got that idea from a chart he found in Nelson's cabin. Chujo shows Tsinchan a copy of an inscription he found in the cave on Baru Island. He kept it secret because he didn't want Nelson to know about it. Key to the inscription is a repeated symbol which Chujo has deciphered as 'Mothra', although he does not know what that means.
The alarm siren again sounds in the jungle of Baru. Drawn to the noise again, the fairies are soon captured by Nelson and his men. The natives again arrive, but this time Nelson is ready. His mercenaries mow down the islanders with submachine guns and make their way back to the ship. One native mortally wounded in the massacre crawls to a cavern temple, pleading to his god Mothra. As the man dies, the rock face crumbles away, exposing an enormous egg.
Tsinchan's editor is furious that the first he has heard of the fairies is from Nelson's publicity campaign. Tsinchan's defense is that everyone decided to remain silent about them, although Nelson has broken that oath. Nelson opens "The Secret Fairies Show" to a packed audience, unveiling this miracle of nature he has discovered. The fairies appear on stage after descending in a tiny carriage lowered by wires. The Shobijin sing before the crowd in their native dialect. In the audience, Chujo and Tsinchan confer. Apparently Nelson funded the expedition to Baru, not the Rolisican government. Both men take note of the name Mothra in the fairies' song.
Back on Baru, the natives also dance and sing; not before an audience but before the enormous egg resting above their temple.
Nelson refuses to allow Michi an interview with the fairies and is having her removed when Chujo, Shinji, and Tsinchan arrive. Chujo warns that Nelson should stop exploiting the fairies and return them to their island. There is too much money involved and the demand is openly mocked. Tsinchan's protest that the girls are being made into slaves is met with a threat of suing him for slander by Nelson's henchman Nakamura. To placate Chujo and assure that the girls are doing their act of their own volition; Nelson allows the group to see the fairies for 3 minutes.
The girls are kept in a large birdcage. Tsinchan tells them that he is their friend and is shocked when they answer him in his own language. Chujo discovers that the fairies communicate by telepathy. The fairies will soon return to their island, distressed by the fact that some of the innocent are sure to be hurt when Mothra comes to rescue them.
On Baru, the natives' prayers and rituals continue in the temple. In answer to the prayers, the egg cracks open, revealing a gigantic worm-like caterpillar.
In Japan, Nelson confronts Tsinchan's editor about the papers less than favorable articles. Just then, Tsinchan interrupts them with a report from the news wire. A huge object has been sighted floating in the South Pacific. Tsinchan states that it is Mothra, a monster that is coming to rescue the fairies. Nelson smugly asks Tsinchan how he knows this. He is not so smug when Bulldog replies that the Shobijin themselves told him.
As the fairies perform for Nelson, Mothra swims toward Japan. Plowing through an ocean liner in her path. At a press conference, nelson denies any responsibility for Mothra's actions. There is no proof that the monster is connected to the fairies. He promises to complain to the Rolisican embassy if Chujo and Tsinchan continue to hound him.
Disgusted, Chujo and Bulldog leave the press conference. They decide to talk to the fairies again. Bulldog fights Nelson's guards, allowing Chujo time to slip into the villain's office and see the fairies. Chujo pleads with them to try and stop Mothra, but the power which guides Mothra to the fairies is beyond their control. As the carriage leaves to take the fairies down to the stage, Chujo realizes that telepathy may be the key.
Chujo and Tsinchan visit Dr. Haradawa, asking him if there is a way to cut off the telepathy. Dr. Haradawa displays a metal which will cut off brainwaves. Putting the fairies inside a box made of this substance would effectively block the telepathic waves.
As Mothra swims still closer to Japan, the military decides to attack. She is heading in a straight line toward Tokyo. Meanwhile, the Rolisican embassy announces that it is backing Nelson.
The JSDF attacks Mothra, dropping napalm bombs and employing jet fighters. Nelson's claim that the attack has killed Mothra is met with doubt by Chujo, Tsinchan and Dr. Haradawa. They impress upon nelson to take the metal box.
At a dam near Tokyo, Mothra reappears. The news of Mothra's survival causes Michi, Tsinchan and Chujo to head to the scene. Meanwhile, Nelson angrily refuses to cancel the performance, telling the fairies that they will never go back to the island. Chujo and Tsinchan watch as evacuees cross a bridge below the dam even as Mothra attacks the structure. Moments before the floodwaters from the burst dam can crush the bridge; Tsinchan races across it to rescue an infant that has been accidentally left on the doomed span.
Chujo finds a note from his son, saying that Shinji has gone to the theater to rescue the fairies. Nelson's guards try to find the boy, but he slips past them. Nelson himself arrives as Shinji tries to escape with the girls. He is soon cornered and subdued. The villains bind and gag the boy.
In the news office, Tsinchan finds out that the Rolisican government is backing down and no longer supports Nelson. Michi and Tsinchan head for the theater, meeting Chujo there. Chujo has come looking for his son. They find Shinji tied up in Nelson's office but Nelson, his men, and the fairies are nowhere to be found. Police and MPs leave, to look for Nelson elsewhere.
Mothra draws closer to Tokyo. The best efforts of the JSDF are futile in stopping the giant caterpillar. The evacuation of Tokyo begins as Mothra barrels through the city, crushing everything in her path. Tanks, missiles and jets are all incapable of harming the huge insect. Mothra's trail of carnage at last brings her to the base of Tokyo Tower. Concentrated artillery seems to at last have an effect and the mammoth caterpillar falls on her back. The military holds their fire as the monster begins to spray silk into the air above her. It is soon obvious that she is spinning a cocoon. There is time now to try and find Nelson and return the fairies before the cocoon hatches.
An all-points-bulletin is put out for Clark Nelson, but the crafty villain is already in disguise and at the airport with two of his henchmen. Nelson passes through the police with a phony passport and boards a jet bound for Rolisica. With Nelson gone, the last chance to settle things peacefully is gone.
To make amends and end Mothra's terror, the Rolisican government is sending Japan its newest weapon - an atomic heat gun. The weapons and their crews will be in Tokyo in the morning. The cocoon is completed and the heat guns are trained upon it. The weapons blast the cocoon, soon setting it on fire. The flames and heat bake the cocoon into a hard shell. The death of Mothra is reported to the world. Even at Nelson's farm in Rolisica, the news is heard, delighting the villains. Now the secret fairies show can go on. Nelson removes the fairies from his suitcase and the metal box. He mocks them, telling them to go ahead and sing, because Mothra can't hear them. Nakamura adds that the reason Mothra can't hear them is because Mothra is dead. The villains laugh as the Shobijin continue to sing.
Back in Tokyo, the scorched cocoon cracks open and a giant moth emerges. Mothra flies into the sky, her powerful wings blowing cars and debris across Tokyo. Chujo realizes that Mothra is flying east, towards Rolisica. He concludes that Nelson must be there with the girls. Now Nelson is a wanted man in Rolisica as well as Japan. The villain still refuses to surrender the fairies, determined to flee to another country. Chujo joins Tsinchan and Michi on a special jet to Rolisica, having been asked by the Rolisican government to negotiate with the fairies when they are found.
Mothra begins her attack on New Kirk City, devastating the metropolis. The Rolisican military proves just as helpless against her as that of the Japanese. Nelson is discovered when his car is blocked by refugees. Angry people surround Nelson, the man who has caused so much misery. Nelson tries to escape on foot, shooting a police officer as he does so. The villain is soon gunned down by other officers, perishing in a hail of bullets.
Chujo, Tsinchan and Michi arrive at the scene of nelson's demise. They realize that they cannot immediately release the Shobijin or Mothra will be drawn right to them. Meanwhile, the destruction of New Kirk City continues.
The tolling of church bells gives Chujo an idea that the symbol for Mothra might be religious in nature. The bells also sound somewhat like the fairies' voices. Chujo impresses on the Rolisican officials to recreate the symbol on the tarmac at the airport and to have every church bell in the countryside ring at three o'clock. It is a desperate gamble, but Chujo prays that it will work.
The sound of the bells draws Mothra away from her rampage in New Kirk City and she settles on the huge symbol painted on the airport tarmac. The huge monster waits expectantly. Chujo opens the case, releasing the fairies. Chujo hopes that the Shobijin will now be able to live in peace. The girls head to Mothra and climb onto their deity. Mothra flies away, headed back to Baru. A good laugh punctuates the event as Michi realizes that she forgot to take any pictures in all of the confusion.
Back on Baru, Mothra and the fairies take up their places in the cavern temple while the inscribed monolith slides upwards, revealing writings which chronicle this part of Mothra's story.