Infant Island, a tropical oasis in the Indonesian Archipelago, was bombarded with massive waves following an asteroid collision in the early 1990's. The torrential climactic shift in the area revealed an enormous egg buried in the side of a hill. An expedition was soon sent to the island to investigate the climactic changes, and it so happened that this small trio discovered the egg during their search of the tiny isle. Even more bizarre, a pair of twin fairies called the Cosmos appeared near the egg. They revealed that over 12 millennia ago, an advanced civilization created a device that could control the weather. The Earth created Battra in order to counter this action, and the guardian Mothra did battle with the creature. Battra was laid to rest in the north seas while the climate controller was destroyed. The land flooded, and Mothra and the Cosmos survived in the mountains. The Cosmos also revealed that Mothra and Battra had reawakened, due to the new dangers facing the planet. Kenji Andoh, a member of the expedition and an employee of the Marutoma Corporation, suggested that the egg should be transported back to Japan in order for it to be properly preserved. The Cosmos put their trust in Andoh, and the egg set sail toward the mainland.

As the ship traveled the long journey to Japan, a powerful pillar of bright blue energy ripped through the surf. Godzilla emerged and approached the colorful orb. In order to keep their vessel safe from Godzilla, Takuya Fujita cut the tethers to the ropes to the egg's transport. Afterward, the egg began to crack and glow. The turquoise eyes of an adorable caterpillar emerged from the broken shell. The larva rushed into the sea to avoid Godzilla's heat ray, and found her way behind the monster. She bit the trunk-like tail, but Godzilla tossed the moth aside. Mothra began to spray her silk at the beast, but she was thrown back yet again by his thermonuclear ray. The persistent insect leaped at the creature, but the massive monster again repelled the diminutive worm. It appeared as though Mothra was in dire straits, if not for the jagged hump that suddenly appeared in the distance. It was the Battra larva, and though it used its horn to maliciously toss Mothra aside, it grappled with Godzilla, unknowingly giving Mothra a chance to escape. As Battra and Godzilla pulled each other under the sea and eventually into a lava flow beneath the Earth's crust, Mothra prepared to return home to safety.

Without the giant egg he had promised to procure, Kenji Andoh kidnapped the Cosmos and handed them to his boss instead. The twin fairies called to Mothra for help, and the mammoth moth inched its way through the endless miles of sea toward Tokyo. As Mothra plowed through the military's defensive procedures, Takuya Fujita absconded with the fairies and attempted to sell them for profit. His ex-wife Masako Tezuka, a member of the expedition to Infant Island, and his daughter pleaded with him to release the fairies... for Mothra was destroying Tokyo in her attempts to rescue her beloved twin fairies. The Cosmos were released, and they ordered Mothra to halt her advance. The obedient Monster turned around and began her long trek home, but she was suddenly fired upon by the military. The military ceased fire when they learned that there were people in the vicinity, but Mothra looked very ill following the assault. She trudged over to the Diet Building, where she raised her head into the sky and shot her silk into the air. The silk gently formed into a soft, protective cocoon. Mothra was about to metamorphosize...!

Wrapped in a blanket of silk, Mothra transformed inside her cocoon. She had come to Japan to rescue her beloved Cosmos, and began her retreat when she learned of their safety. The military, however, fired on the larva. When a cease-fire was issued, Mothra looked very lethargic. She slowly made her way to the Capitol, and wrapped herself in a protective cocoon.

Meanwhile, the pressure of the magma flow beneath Mt. Fuji began to reach a critical level. Suddenly, Godzilla emerged from the volcano! It was believed that the menace had died in an erupting lava flow beneath the sea, but it turned out that he merely swam through the molten rock to his present location. The saurian shadow, pulsing with anger, began his descent toward Yokohama.

As Godzilla was emerging from his fiery tomb, the furry shell of Mothra's cocoon began to stretch and tear. Two beautiful, cerulean pools pierced through the night, as a pair of plush wings began to unfold. Mothra began to fly into the night, for it was her duty to destroy her dark counterpart: Battra.

It was thought that Battra had died earlier in a lava flow in the ocean depths, but the reddish glow on the surface of the sea burned a flame of doubt on this assumption. Battra rose from the surf and immediately transformed into its imago form in a blaze of energy. It sought to destroy its mortal enemy Mothra, and flew toward the mainland.

At Yokohama Cosmo World, the park goers gazed into the sky as Mothra and Battra clashed above the city. Battra pursued Mothra with his deadly eye beams, and in the process, the indifferent insect caused the collapse of the Yokohama Bay Bridge. Mothra crashed into the ground, and her archenemy's eye beams continued to fire. Before Battra could continue the onslaught, though, he was suddenly distracted by another monster; Godzilla had arrived on the scene. Battra, recognizing the threat that this new entity posed, proceeded to fire his eye beams at the nuclear menace. In the process, the dark moth destroyed the Yokohama Landmark Tower, sending the once proud structure crashing onto his furious foe. Battra flew to the ruins where Godzilla lay, but the devious creature beneath the rubble released his nuclear pulse. Godzilla regained his balance and tossed Battra into the distance. A nuclear ray quickly followed the physical assault, and Godzilla's foe was rendered incapacitated.

Mothra, understanding the futility of the current battle strategy, shot Godzilla with her antenna beams and descended to meet Battra. They communicated and agreed to cooperate. Mothra began to revive Battra, but Godzilla interrupted the process. The determined moth left Battra to fight her true foe. She reflected his attacks with her glimmering scales, but the terrible titan's nuclear pulse sent the majestic moth crashing underneath the Cosmo Clock 21 Ferris wheel in the theme park. Godzilla fired a blast at the Ferris wheel, and it began to tilt and fall toward the immobile creature. Battra caught the amusement ride just in time, and sent it crashing into Godzilla instead. Regaining her composure, Mothra created a bright shield of energy around Godzilla as her ally fired his eye beams at the monster. Godzilla continued to fight on, and in the process destroyed the Yokohama Grand Intercontinental Hotel. The reptile's reign of terror was finally over, however, when the monster was sent crashing into the ground. Mothra and Battra communicated once more, and they made a pact. The former latched onto Godzilla's tail as the latter grabbed onto Godzilla's head and neck. They slowly lifted the detestable behemoth into the air, and they carried him out to sea. However, Godzilla sank his teeth into Battra's neck and used his thermonuclear ray on the creature's wound, which was flowing most repulsively with yellowish blood. Eventually, Battra's eyes lost their glow; the creature had died. Mothra released Godzilla's tail, sending her ferocious foe and her late ally into the depths of the sea. The majestic moth sealed the area with a special energy, and departed for the mainland.

It so happened that the year 1999 was going to bring an asteroid plummeting to the planet. Battra was going to be the one to destroy the massive meteor before it collided with Earth, but since he had died in the battle with Godzilla, Mothra would have to halt its approach in his stead. After all, the two monsters had made a solemn pact. After saying their goodbyes to humankind, the Cosmos departed. They joined Mothra and flew into space, for they were about to save the Earth yet again...