After the mummified corpse of the demonic Gigan was uncovered in Japan, two mysterious fairies submitted a grave warning to three humans overlooking the remarkable discovery. These "Shobijin" teleported the humans to a remote cave, and sternly warned that Gigan must be returned to his burial chamber, lest the world fall to ruin at the hands of the mechanized monstrosity. It was revealed that a guardian monster named Mothra had defeated Gigan ten millennia ago, and that these two monsters should never battle again, for the consequences would be terrible. The Shobijin returned their guests to the mummified Gigan, but the fairies' warning was not taken seriously. Gigan was not returned, and ultimately, it was reborn!

Following a long war between Godzilla and an army of monsters released by a race of evil aliens called the Xiliens, an asteroid named Gorath began to plummet toward the Earth! In response, the Shobijin summoned the majestic Mothra to stop the devastation that this newly arriving force would bring. She began to soar gracefully to Tokyo, where she would encounter new dangers, and a powerful old foe...