The restless souls of those who died in the Pacific War accumulated into Godzilla, a detestable demon that attacked Tokyo in 1954. In 2001, as hellish horror was returning, the spirit of Hiyotoshi Isayama began to release the Guardian Monsters of Japan's ancient past.

A small group of eleven young cyclists arrived at Lake Ikeda in Kagashima. Though their intentions seemed harmless at first, their demeanor began to quickly turn sour. The deviants ransacked a local store. Even worse, when a barking dog irked the troublesome teens, they heartlessly prepared to do away with the poor pooch. Amidst the chaos of the break in, an odd antiquity was overturned. The humanoid statuette fell on its side, and the reveling vandals prepared to hand the artifact the same fate as the animal they had shoved so carelessly into a cramped receptacle. As this insanity continued, a mysterious old man watched the situation from the edge of a dark forest.

The laughter and revelry continued to echo into the night as a boat departed from the shore, bent on a malicious mission. The vessel was suddenly overturned, and the helpless humans were quickly tugged into the deep, one by one. The mortified onlookers stood speechless as what appeared to be an enormous boulder broke through the surface of the once placid lake. Mere moments passed before the terrible truth was realized: the enormous object was a monster! A piercing roar bellowed from the creeping creature as it barrelled its way closer and closer to the shore. The shrieking silhouette struck panic into the hearts of the onlookers. Mothra, as the ancient Guardian Monster was called, killed each and every one of them by entrapping them in her silky cocoon. The lucky pup managed to escape this terrible fate. Like a blanket, the abominable arthropod enshrouded herself in her own silk, for she needed to metamorphosize in order to confront the approaching danger...

The people on the shore of Lake Ikeda gazed with curiosity at the enormous cocoon that sat motionless in the calm waters. The Guardian Monster Baragon had been ruthlessly slaughtered by Godzilla in the Owaku Valley in Hakone, and the despicable beast was now inching its way closer and closer to Tokyo. The sun set over Lake Ikeda, and Baragon's replacement quickly grew inside the shell of her protective pupa. An expressionless face suddenly tore its way through the protective coating, and two purple gems stared deep into the night. Mothra, the second Guardian Monster, climbed atop her broken cocoon, and her membranous wings began to materialize into a beautiful rainbow of vibrant colors. Her wings moved with a smooth motion as she prepared to take off. Into the sky she soared, prepared to confront her saurian foe, Godzilla.

As the final Guardian Monster, Ghidorah, appeared near Mt. Fuji, Mothra arrived in Yokohama. Mothra landed atop the Yokohama Landmark Tower, the nation's highest skyscraper. She peered down on the dimly lit metropolis, seeking the creature she was awoken to exterminate. Godzilla and Mothra exchanged chilling roars. The mammoth moth started to glide gracefully from the pinnacle of the building. She swam on the breeze, gently and elegantly boasting her prowess in the sky. Grace soon gave way to raw power as the mystifying monster fired her projectile stingers into Godzilla. The organic daggers exploded on contact, but they managed to cause only minimal damage. The monster king countered this stinger barrage with his heat ray, and Mothra swiftly picked up speed to escape the speeding stream of searing-hot plasma. In the process of escaping the nuclear hellfire, Mothra led the beam straight into the Landmark Tower. In a flash, the once proud symbol of human ingenuity became a towering inferno. In the chaos, Mothra managed to silently descend behind Godzilla and latch tightly onto the skull of the nuclear menace. When Ghidorah appeared on the scene, Mothra humbly retreated to allow the third Guardian Monster to enter the fray. The intelligent insect managed to again align herself silently behind Godzilla while he was preoccupied with Ghidorah, but alas, the blunt blow of Godzilla's tail sent the moth flying into a furious tumble. She regained her balance and soared again into the sky. Ghidorah was suddenly knocked unconscious by the superior, surging strength of his sadistic enemy. As Godzilla attempted to fire a final radioactive ray at Ghidorah, Mothra came to her fellow Guardian's defense and took the full force of the powerful beam. With both Mothra and Ghidorah seemingly defeated, the military fired on the lumbering leviathan. Unfortunately, the self-defense force did not last long against the horrendous heat ray. Upwards of ninety percent of the counteroffensive was destroyed by Godzilla's wrath, and it seemed as though nothing could be done to gain an advantage over this cyclopean creature.

Her wings ablaze, Mothra rose from the ruins of the city. Her expressionless face gazed deep into the twisted soul of the radioactive reptile. She approached Godzilla from behind, but Godzilla was prepared. He turned and fired the full force of his thermonuclear breath, dematerializing the once majestic moth. Mothra's energy swirled and started to descend upon Ghidorah. His eyes opened, and the final Guardian Monster returned in full furious force as King Ghidorah!