The meteor comes to Earth but it does not go unnoticed. A group of scientists spots it and sends a climbing party to investigate. They set up camp adjacent to the meteor to take recordings. 

Meanwhile, a princess from another country flees by way of aircraft to Japan, fearing that certain seditionists are out to kill her. Unknown to her, a bomb ticks the seconds by in the cargo bay. She has a locution that warns her to jump from the plane and she listens. She jumps from the plane just in time before it explodes. She falls into the ocean unharmed. 

The police presume the princess dead until a prophetess dressed in rags appears and starts to warn the populace that Rodan is coming back. The officer assigned to guard her, Shindo, is at home reading the paper when he recognizes her as the princess. The princess-turned-prophet goes to the volcano and warns the populace that Rodan is about to break out of the earth's crust. Of course, no one listens until it happens.
She then goes to the boat that is taking the twin fairies back to Infant Island and warns the captain not to set sail. The annoyed captain puts her ashore and sets sail anyway, only to have his ship blown to pieces by Godzilla later in the movie.
Shindo's sister Naoko takes the princess to a hotel where the thugs who are out to get her are standing in the hall. Anyway, they try to kill her throughout the film. The princess tries to tell everyone that she is of Martian descent and that long ago, a space monster called Ghidrah ravaged the planet until there was nothing left. She then warns that Ghidrah has come to Earth to do the same thing it had done to Mars.
At that moment, the meteor explodes and starts spewing energy. The energy materializes into a giant, gold-colored three headed dragon with two tails. Ghidrah heads for the nearest Japanese city and proceeds to rip it apart.
Godzilla and Rodan are also in Japan fighting it out between them. When asked by the government the fairies (who listened to the princess and skipped out on the ill-fated sea voyage) called Mothra to help. Mothra swims to Japan and tries to make peace between the warring kaiju. Godzilla and Rodan tell Mothra to mind her own business, and then continue fighting. 
Mothra gives up and goes to fight Ghidrah by herself, which startles both Rodan and Godzilla into paying attention. Mothra almost has her butt handed to her when Godzilla and Rodan come to her defense. 

Ghidrah is a considerable foe, and it takes the three of them against their thrice-headed enemy to proclaim victory for the earth. Ghidrah is sent packing. During the course of the great battle, the thugs try to kill the princess one last time. It comes down to a shooting match between Shindo and the lead seditionist. Just as the princess' enemy is about to kill both of them with a gun, he catches a huge boulder square in the chest and plunges to his death. The princess returns to her home, and the fairies and Mothra return to theirs with Godzilla and Rodan looking on. Everything is peaceful once again....until the next time.

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