Reporter Naoko Shindo observes members of a UFO club searching for flying saucers on an unusually warm winter night. Having failed to spot any UFOs, they accuse Naoko of being a non believer and the reason why they haven't spotted anything. As Naoko inquires further, the head of the club comments on how many strange phenomena have been occurring across the globe and is concerned something terrible might happen to the Earth. They are interrupted by a meteor shower as Naoko's brother, Detective Shindo, also witnesses the phenomena. Shindo is then given an assignment by his chief of police. He is to act as a bodyguard for the princess of the small kingdom of Selgina, Maas Doulina Salno. Salno is en route to Japan to escape political opposition that seeks to assassinate her. However as her plane flies to Japan, Salno becomes possessed by a mysterious voice and jumps out of the plane, which is subsequently blown up by a bomb. The night ends with a large meteor landing in Kurobe Valley.The following day, Professor Murai and his team arrive near Kurobe Dam and set out to investigate the meteor that crashed the night before. As the group hikes through the mountains, they notice that all their compasses have started to malfunction. When they reach the meteor, they are surprised to observe it emitting a powerful magnetic force.Shindo inquires with his chief about Salno, only to be told that she was assassinated before she could arrive in Japan. Elsewhere, Naoko is alerted about a mysterious prophetess who is making an ominous prediction of Earth's destruction. Naoko arrives on the scene and attempts to ask the prophetess where she is from. She claims to be from Venus and warns that the Earth's end will begin with a strange event on Mount Aso. Despite her warnings, most people scoff at her claims. Later that night, Shindo arrives at his mother's house and notices Naoko being dropped off by Professor Murai. Inside, Naoko, Shindo, and their mother, tune into the "Where Are They Now" TV show. On the program the Shobijin, Mothra's fairies, introduce themselves to the audience. Lamenting the death of one of the twin larvae, the fairies sing a melody as Shindo turns to a newspaper. He is shocked when he sees a picture of the prophetess and notices a striking resemblance to princess Salno. Salno's political opposition in Selgina is also surprised to learn that the princess is alive. Salno's assassin, Malmess, is sent to Japan to finish the job, or he himself will be killed.Back in Japan, Naoko is instructed to follow Salno while Shindo asks his chief to let him pursue the case. Shindo meets up with Naoko and they head out for a drink where they meet up with Professor Murai. As Murai discusses his findings with the two, they see a news report that shows the prophetess speaking at Mt. Aso. Salno warns the crowds that volcanic gases will resurrect Rodan. As her warnings fall on deaf ears, Rodan emerges from the crater and takes flight as the crowds flea. The assassins arrive in Japan while Professor Murai is back in Kurobe and notices that the meteor appears to be growing.Salno reappears at a port where the Shobijin prepare to board a ship back to Infant Island. As Salno warns that the ship must not sail, she is approached by Naoko and is invited to join her at a hotel. Malmess and the other assassins follow the two women. As Naoko discusses with Salno, they discover that the Shobjin have heeded Salno's warnings and did not board the ship. It is soon revealed that Godzilla has reemerged and destroyed the ship.Back at the hotel, Naoko gives Salno a change of clothes and steps out of the room to meet her brother in the lobby. Malmess and his men take the opportunity to enter the room and verify that the prophetess is the princess. As Malmess pulls out a knife and is about to kill Salno, the Shobijin cut the lights and warn Shindo and Naoko. Shindo opens fire on the assassins and chases them off. The two make sure that Salno is safe when they hear a large explosion coming from the harbor. Godzilla has entered Yokohama and spots Rodan in the sky. Infuriated, Godzilla proceeds to chase Rodan across Japan.The next day, Shindo brings Salno to the laboratory of Dr. Tsukamoto, a brilliant psychiatrist who attempts to diagnose the princess. The treatments however seem to be ineffective as Salno still claims to be from Venus and makes one final prediction. The Earth will meet its end with the arrival of King Ghidorah, a powerful space monster who completely annihilated the civilization on Venus. Salno claims Venusian heritage and explains how a few of them survived and assimilated amongst humanity while still retaining some of their abilities.Godzilla has followed Rodan to Mount Fuji, where the two monsters continue to bicker with each other. Back in Kurobe, Murai and his team notice strange activity from the meteor. Suddenly, the meteor splits open and an explosion of flames bursts into the sky. The flames materialize into the golden three-headed dragon, King Ghidorah.With Godzilla, Rodan, and King Ghidorah loose in Japan, the government assembles an emergency meeting at the National Diet Building. Naoko and Murai arrive with the Shobijin and propose a plan to ask Mothra to help defend the world from King Ghidorah. While the Shobijin wish to help, they fear that the Mothra larva will be unable to defeat King Ghidorah. Their only hope is to have Mothra persuade Godzilla and Rodan to set aside their differences and join forces to help save the world from the space monster. Just then, Ghidorah flies over Tokyo and causes great damage with his gravity beams. The assembly beg for the Shobijin's help. They oblige and pray on Mothra to arrive from Infant Island.Back at Dr. Tsukamoto's laboratory, the doctor prepares to administer Salno electroshock therapy. Tsukamoto instructs Shindo to set the voltage to 500 volts. However, Malmess and the other assassins sneak in to the lab an set the voltage level to a lethal three thousand volts. Just before the electrical shock can be administered, Rodan lifts Godzilla into the air and drops him onto a power pylon, knocking out the power and unintentionally saving Salno. Malmess and his men burst into the lab and get into a shoot out with Shindo. Naoko and Murai arrive to the sound of gunfire as Shindo chases off the assassins. As Godzilla and Rodan continue to squabble with one another, Naoko and Murai join up with Shindo, Dr. Tsukamoto, and Salno. The group drives off as Mothra arrives to the base of Mount Fuji. They exit their car and climb up a hill where they witness Mothra break up the fight and attempt to talk to Godzilla and Rodan. The fairies translate as Mothra attempts to persuade the monsters to join forces and save the Earth from King Ghidorah. However, Godzilla and Rodan refuse, saying that it's none of their concern. Godzilla says they have no reason to help humanity as humans have always bullied then. To which Rodan agrees.The assassins make their way through the mountain roads when they are caught in a landslide caused by Ghidorah. Their car is crushed with all the assassins, except for Malmess, killed. As Mothra continues her conversation, Shindo and the rest decide to head to safety and move to higher ground. Mothra pleads with the monsters, arguing that the Earth doesn't just belong to humanity, it is theirs too and they should defend it. However, Godzilla and Rodan fail to agree and Mothra is forced to head out and confront Ghidorah all by herself.Ghidorah quickly overpowers Mothra, and is repeatedly blasted by the space monster's gravity beams. Inspired by the larva's courage, Godzilla and Rodan finally decide to join Mothra in the battle against King Ghidorah. As the monsters of Earth struggle against Ghidorah, Shindo notices that Salno has disappeared. The group splits up to search for her when Malmess discovers her praying in a gorge. Malmess proceeds to open fire on the princess when Shindo arrives to save her. Salno collapses further into the gorge as Shindo descends to reach her. As Malmess reloads, Salno comes to her senses and recognizes him as a traitor. Shindo pulls Salno aside to defend her, but he shot and disarmed by Malmess. Just as the assassin is about to kill them, a blast from King Ghidorah's beams strikes the mountain and causes a landslide that sends Malmess plummeting to his death. Tsukamoto and the others soon arrive to help take the injured Shindo and princess to safety.The Earth's monsters continue to battle Ghidorah and use their distinct abilities in a collective effort to take the upper hand against the space dragon. Godzilla takes the brunt of Ghidorah's attacks as Rodan lifts Mothra in the air to cocoon the dragon in silk. Battered, King Ghidorah proceeds to take flight and flee as Godzilla, Rodan, and Mothra emerge victorious.With the Earth safe, Shindo, Naoko, Murai, and Tsukamoto, arrive at an airport to bid Princess Salno farewell. Salno asks Tsukamoto how she regained her memory, to which he replies it must have been the shock of being grazed by a bullet that caused her to regain consciousness. She then wonders if her abilities will ever return, with Tsukamoto responding that such matters are beyond our understanding. Salno approaches Shindo and thanks him for saving her life three times. Shindo asks how she can remember, with Salno responding she is only able to recall the moments he saved her life. Salno expresses her gratitude and assures Shindo that she will never forget him, with Shindo wishing her a prosperous life and bidding her farewell. As Salno's plane returns to her kingdom, Godzilla and Rodan watch from afar as Mothra and the Shobijin head back to Infant Island.