A year has passed since Kiryu repelled Godzilla from destroying Tokyo. US and Japanese forces are challenged by a huge UFO which appears on their radars, coming dangerously near to the Japanese islands. At his country home, Professor Shinichi Chujo (Hiroshi Koizumi) and his nephew Yoshito Chujo (an Engineer in the Kiryu Squad, played by Nobuko Kaneko) are visited by Mothra and the Shobijin, who trust the elder Chujo because he understands them and tried to help them back in 1961. They implore the professor to convince the Japanese Government to return the original Godzilla's remains to its watery grave. This is because all life is sacred, and unless this is done soon, Mothra will turn against humanity.

  

Professor Chujo makes an appeal to his old university colleage, Prime Minister Igarashi (Akira Nakao)to abandon the Kiryu Project, and send the Godzilla skeleton back to its resting place. Meanwhile, the carcass of Kameba, a giant turtle-like creature, washes up on the shores of Kujukuri Beach in East Chiba Prefecture [this is where the great ape came ashore in KING KONG VS GODZILLA], and all contact with a nuclear submarine in the Pacific Ocean is lost. Finally, a still- wounded Godzilla appears off the coast of Japan and lands in Tokyo. The special forces of the JXSDF counter Godzilla's attack in the Shinagawa Ward using only its Maser Cannon batallion -- the badly damaged Kiryu is not yet fully operational and cannot be sent into battle. As the situation becomes grim, Professor Chujo attempts to summon Mothra to fight Godzilla by employing a similar method used to calm the giant moth in its attack on New Kirk City, 43 years earlier...