Oblivious to the fearful fate that the scientific community sees coming upon the Earth, an archeologist named Takuya Fujita is poking around in the ancient ruins of a shrine in faraway Thailand. After he finds an ancient idol, the shrine begins to fall into rubble all around him. Takuya barely escapes with his life...and runs into another problem: the Thai army who are unappreciative of Takuya's thieving. 
Takuya is arrested and gets himself tossed into a Thai jail. Later on he receives three visitors: Dobashi, from the Security Agency; Andoh, with Marutomo Corporation; and Masako Tezuka, Takuya's ex-wife. Takuya is promised freedom in exchange for exploring an island near Indonesia. Takuya goes with Masako and Andoh to a small isle called Infant Island. The three brave rotten wood bridges, raging rivers and rugged tropical jungles before they find a cave. Exploring the cave, they find a cave painting; on further exploration, they find an exit and the prize: a huge egg. 

To their astonishment, they find they are not alone on the island: a pair of six-inch twin girls called Cosmos are the tiny guardians of Mothra, the god worshiped by the now-nearly extinct Cosmos civilization. The Cosmos explain that when their scientists began to tamper with nature, the earth created a monster named Battra which attacks and destroys anything which threatens the Earth. Mothra and Battra fought and Mothra sunk Battra into the ocean, though not before Battra smashed the weather control system and unleashed the forces of nature on the hapless Cosmos. They warn the three that Mothra's egg appeared because the Earth is in danger and that Battra has also awoken. 
The Cosmos agree to cooperate with Masako and Andoh and Takuya, and also to allow the egg to be taken to Japan. The egg is loaded onto a barge trailing behind a ship. The ship leaves Infant Island and sets sail for Japan. 

Meanwhile, the scientists pick up a wake slicing through the water toward Japan. At first they assume it's Godzilla but one of them confirms that it is Battra. Battra comes ashore and destroys a few city blocks; then, unaffected by the military firing on him, disappears into the ground. 

The ship carrying the Cosmos and the egg picks up something huge on their radar. The radar blip turns out to be Godzilla! He's come to fight Mothra; either that, or else have a Mothra omelette. A determined Takuya goes underneath to release the ropes towing the barge, even getting into a fistfight with Andoh, who wants the egg for the C.E.O. They roll around on the deck just like a couple of six year old boys. Takuya manages to give Andoh a black eye before they are interrupted by the egg glowing and cracking. Takuya releases the barge tow as Andoh looks on in amazement. The egg hatches, and the newborn Mothra larva hits the water just before the barge is wiped out by Godzilla. 
The two go head to mandibles in battle with Mothra hiding behind the barge. No sooner had Godzilla flung Mothra off his tail and into the water than Battra shows up and throws Mothra out of the way. Battra and Godzilla fiercely attack one another. The two continue their battle underwater as Mothra swims away, back toward Infant Island. 
Battra and Godzilla are tearing at each other underneath the surface of the ocean. The force of their battle resulted in the cracking of the ocean bed, causing Godzilla and Battra to be pulled into an underwater volcano.

Takuya, Masako, Andoh and the Cosmos end up in Manila in the Phillippines. In the morning, Masako discovers the Cosmos missing. Andoh has taken the Cosmos back to his boss Tomokane, who has big plans to use the Cosmos for his own personal gain. The Cosmos, not wishing to be prisoners to Tomokane nor line his pockets, turn to Mothra for aid. 
Mothra swims toward Tokyo to rescue his little friends. Takuya steals the Cosmos from under Tomokane's nose and tries to sell them for a million dollars. Masako becomes angry when she catches him with the Cosmos in a wicker box. She and their daughter Midori persuade their husband and father to do the right thing and not sell the Cosmos.
Just then Mothra shows up and starts to tear down the building they are in. Midori asks the Cosmos to please stop Mothra, promising them that she will stop her Daddy from stealing. The Cosmos reassure Mothra that they are all right. Mothra, satisfied, turns around and goes to the Diet Building; he starts to spin a cocoon. 
Mt. Fuji begins to erupt, and Godzilla comes out of the lava. He goes toward Tanzawa after tearing up Yokohama. Battra also appears from the ocean. After a burst of energy he transforms into his flying form and goes to Japan to attack Mothra. 
The Cosmos start to sing to the cocoon, which hatches as the crowd looks on, to reveal a huge moth with beautifully colored wings. Mothra leaves to fight Battra. As the astonished populace looks on, Mothra and Battra batter-ram one another in the sky.
Godzilla shows up on the scene and Battra fights Godzilla. Godzilla defeats Battra. Mothra goes to Battra's side and heals Battra. Mothra then gets up and almost loses his own life to protect Battra from Godzilla's attack. Battra and Mothra team up to defeat Godzilla. 
Battra and Mothra succeed in carrying Godzilla away from Japan, but Battra, which is injured when Godzilla bites him, is wiped out by a point-blank atomic breath blast. Mothra lets go and lets Godzilla and Battra fall into the ocean, and forms a sort of energy cage to temporarily contain Godzilla.
The Cosmos thank the humans for everything they've done. They tell the humans that a meteor is headed toward Earth that will wipe it out. Since Battra is not around to do his job of defending the Earth, Mothra must fly into space. The Cosmos levitate into air; then, with one last wave, they transform into spirits and hide themselves in one of Mothra's feelers. Mothra serenely flies off into space. 

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