Twelve millennia ago, a guardian named Mothra roamed the Earth as an advanced civilization, the Cosmos, foolishly crafted a machine that could control the weather. Offended, the Earth created a dark Mothra, Battra, which destroyed everything that endangered the planet. After a fierce battle, Mothra vanquished Battra, and he was put to rest in the Northern Sea. In the process, the climate controller was destroyed, and most of the land on Earth remained underwater due to intense flooding. Mothra survived and retreated into the mountains with the surviving Cosmos...

In the year 1993, on Infant Island in the Indonesian Archipelago, the Cosmos appeared to Takuya Fujita, Masako Tezuka, and Kenji Andoh and revealed their tragic past. They also revealed that Mothra was now in a new life cycle, and that the egg of Mothra was on their island. Both Mothra and Battra were revived in response to the reckless destruction of nature at the hands of humankind, including the actions of such big businesses as the Marutoma Corporation. Kenji Andoh, an employee of said corporation, suggested that the egg could be better preserved in Japan, and the Cosmos agreed. As they sailed to Japan, Godzilla emerged from the ocean and attacked the enormous egg. The monster became sidetracked however, as the recently rejuvenated dark Mothra, Battra, became locked in combat with Godzilla. As their terrible battle continued, they fell into a fissure in the Earth's crust beneath the ocean, and as they sank in the magma flows, they were presumed dead.

Mothra returned to Infant Island as the Cosmos arrived in Japan. Kenji Andoh absconded with the fairies and handed them over to his CEO, Takeshi Tomokane. Now in captivity, the Cosmos were left with only one option: to call for much-needed assistance. They sang into the distance and pled with Mothra for rescue. Leaving her island home, Mothra rushed to Tokyo, where she began to destroy everything in her predetermined path to rescue her beloved fairies. In the meantime, Takuya Fujita cunningly kidnapped the Cosmos and attempted to extract one million dollars in ransom from the Marutoma Corporation; however, his ex-wife and daughter began to convince him of how wrong this course of actions truly was. As the argument continued, Mothra finally arrived, and the hotel in which the humans stood began to tremble. Takuya finally relented, and the Cosmos were freed. Upon convincing Mothra that they were fine, she began to retreat. Unfortunately, the military was unaware of this change in events, and when their forces were finally in position, an all-out assault commenced. When the Self-Defense Force was ordered to cease fire, Mothra began to act very lethargic. She slowly made her way to the Diet Building, where she enshrouded herself in silk and began to form a chrysalis. The CEO of the Marutoma Corporation ordered Kenji Andoh to use this opportunity to reacquire the Cosmos, but he resisted and was ultimately terminated. Left alone, the CEO could was left to wallow in his own shame. As the night progressed, the Cosmos sang again, as an adult Mothra emerged from her pupa. The two fairies revealed that Mothra was going to locate and destroy Battra. Godzilla and Battra were both still alive...

Having survived the magma flows, Godzilla emerged at Mt. Fuji as Battra emerged from the ocean floor, metamorphosizing instantly into its imago form. Takuya Fujita, Masako Tezuka, their daughter, and the Cosmos drove to Yokohama, where they witnessed an intense war of the monsters. Battra pummeled Mothra into submission, and it appeared as though she would lose this fight; however, Godzilla suddenly appeared, and this new contender distracted Battra's attention. Unfortunately, Godzilla proved to be a much greater challenge, and Battra was thrown to the ground below. In response to this new, nearly invulnerable hindrance, Mothra rose from the streets and repelled Godzilla as she made her way to Battra. The Cosmos sang once more as Mothra bestowed energy into her old enemy. Reentering battle, Mothra fired her full arsenal at Godzilla, to no avail. Luckily, Battra saved Mothra just in time, and the Cosmos revealed that the two nemeses were now allies. Joining forces, Mothra and Battra subdued Godzilla and lifted him over the sea. Alas, Godzilla killed Battra in the process, and Mothra was forced to drop both monsters into the cold ocean below, upon which she sealed her energy.

When Mothra returned to her fairies in Japan, it was revealed that Battra was to stop an asteroid from plummeting to Earth in 1999. Now that he was dead, it would be up to Mothra to save the planet from the incoming meteor. The Cosmos lifted into the air and rushed to join Mothra. The majestic moth and her fairies soared into space, ready to meet their destiny.

Two years passed as Mothra flew through the vast emptiness of space, determined to halt the incoming meteor. A new and deadly power was discovered as Mothra pierced through the dark void, and a Fairy Mothra was dispatched to planet Earth, which the Cosmos used to submit two solemn warnings to psychic Miki Saegusa. It would be necessary, they instructed, for her to assist in the defeat of this new monster, and it was imperative that the whole world join together in the destruction of the space creature. SpaceGodzilla, as it came to be known, appeared on Earth and entrapped Godzilla's offspring in a crystal prison. Moguera, G-Force's replacement for Mechagodzilla, and Godzilla both aided in the defeat of this beast. With SpaceGodzilla defeated, the Cosmos thanked Miki and Fairy Mothra returned to space where they could finish their mission to save planet Earth.