The tranquility of the bubbling clouds was suddenly shaken when an unseen force began to tunnel through the endless mass of vapor. Two F-15s were dispatched to intercept the unidentified flying object, but despite how hard the pilots tried, they could not identify exactly what was barreling through the sky. The two aircraft began to fire on the object when it wouldn't respond to their signals, but something strange occurred. The pilots suddenly heard singing, and in the chaos that followed, contact was lost with both of the jets.

Thirteen days later, the unidentified object landed near a cottage in Karuizawa. It brought with it two tiny fairies called the Shobijin. They were there to submit an ultimatum, and they chose Shin'ichi Chujo to deliver the following message to the rest of humankind: if the original Godzilla's bones, which were built inside the cyborg Kiryu, were not returned to the sea, the monster Mothra would declare war on civilization. If, however, the bones were returned to the sea and Godzilla still attacked, Mothra would protect the people. Outside the cottage, Shin'ichi witnessed the flight of the once unidentifiable object that had carried the fairies. The UFO was Mothra, the same creature that had attacked Tokyo 43 years earlier.

Shin'ichi Chujo traveled to Tokyo, where he warned Prime Minister Hayato Igarashi that the Kiryu project had to be abandoned. The Prime Minister, skeptical of Chujo's story and fearful of Godzilla's ever-present threat to the nation, believed that such a move would be suicide. Unfortunately, Godzilla was already beginning to make his presence known again. He killed a monstrous sea turtle named Kamoebas and destroyed a US nuclear submarine off the coast of Guam. The burly behemoth suddenly emerged at sea, and battle cruisers began to fire on the monstrosity as he continued along his predetermined path to Tokyo! The bustling metropolis was evacuated, and Godzilla began to push his way into the heart of the city. He was heading straight for the bones of his predecessor, locked within the mechanical dragon Kiryu!

Meanwhile, Shin'ichi's grandson, Shun Chujo, had rushed to his now abandoned school. Using an amulet that the Shobijin had left behind as a guide, he arranged a group of desks in the courtyard in a way that resembled a symbol significant to Mothra. When Shin'ichi finally found his grandson at the school, the young boy was just finishing his rendition of the symbol. A shadow darkened the courtyard momentarily, and in the sky, Mothra swam through the air like a majestic bird. She flew around Tokyo and her silhouette cast against the beautiful sunset. The guardian moth scraped Godzilla with her wing, and she began to create hurricane winds. Amidst the confusion of the swirling dust, Mothra grabbed Godzilla and built momentum as she dragged the nuclear menace through the city. She released her grip, and Godzilla was sent crashing into the ground. When Godzilla arose, Mothra again latched onto his head, but her ferocious foe chewed off one her legs with his razor-sharp teeth. The desperate moth began to release the scales from her wings, and she reflected Godzilla's thermonuclear ray back to its source. Unfortunately, Mothra's loss of scales would eventually cause the deterioration of her wings, and ultimately she would not be able to sustain lift. Godzilla again fired his breath as Mothra dodged, and the highly destructive beam left Tokyo Tower in ruins. Another thermonuclear ray suddenly damaged Mothra's right wing, and she fell to the ground, struggling to regain lift. As Godzilla approached the helpless creature to finish her off, Kiryu suddenly arrived. The massive monster and his cybernetic clone fought savagely, but after a long exchange of attacks, Kiryu found itself lying relatively helpless on the ground. When the machine was about to endure the force of Godzilla's ray, Mothra used some of her last ounces of strength to intercept the beam. With her left wing now injured, it appeared as though she could no longer regain lift. As she fell to the streets yet again, Kiryu managed to regain its composure and reenter the fray.

Finally, cavalry arrived in the form of Mothra's offspring. The larvae had very recently hatched from a mammoth egg, which Mothra had laid in the Bonin Islands weeks earlier. While one larva distracted Godzilla with its silk spray, the other began to communicate with Mothra. The larva that had faced Godzilla was grazed by the monster's breath, and its sibling rushed to assist. Both creatures returned to further communicate with their mother. Godzilla, however, was charging a nuclear ray in order to destroy Mothra and her offspring. The selfless, heroic guardian rose into the air and endured the full fury of the beam. Mothra erupted in flames and burst into a massive explosion. The now crimson eyes of the Mothra larvae were glowing with hatred for their enemy, for they craved retribution for this injustice...