Forty-three years after their first appearance in Japan, the Shobijin arrive at their old friend, Dr. Shinichi Chujo's, country home. The Shobijin request that Chujo tell the Japanese government not use Godzilla's bones as a fighting machine, and to return them to the sea. The Shobijin explain that Mankind should not touch the souls of the dead. If the government does not return the bones to the sea, then Mothra will turn against them, even though she does not want to. The next day, Chujo visits his friend, Prime Minister Igarashi, and tells him of the Shobijins' request. Igarashi feels he must decline; he must protect Japan from Godzilla. Godzilla soon arives in Shinagawa. Chujo's grandson, Shun, who has heard all about Mothra from his grandfather, takes the stone platee with Mothra's symbol that the Shobijin left. Shun recreates the symbol in a schoolyard using tables and chairs. Eventually, Mothra arrives in Japan, to fight Godzilla. Mothra surprises Godzilla by hitting him on the head, and then flaps her wings creating winds strong enough to knock Godzilla back. Mothra then grabs Godzilla by the neck, dragging him through the streets sending him crashing into buildings. Mothra then lsprinkles a yellow powder from her wings. Chujo, standing next to his grandson, explains that, "Mothra's time to die may have come. The Poison Powder Attack is Mothra's final weapon..." Meanwhile, the Shobijin begin singing to a giant egg, which eventually hatches. Much to the Shojobin's surprise, two Mothra caterpillars emerge, instead of one. The caterpillars immedietely head to Shinigawa, to help their mother in battle...