In Tokyo, reporter Naoko Shindo waits on a rooftop with a club of 'scientific' saucer enthusiasts for the arrival of UFOs. The club finally decides that the saucer people are not coming, having detected Naoko's doubting mind. Suddenly, bright objects are sighted in the night sky. The scientist leader of the club declares it to be a false alarm, nothing but a meteor shower. One meteor crashes in the remote Kurobe Gorge.
Meanwhile, Naoko's brother, a Tokyo detective, is told by his superior Okita that he is to go to the airport and await the arrival of a VIP, the Princess Selina Salno of the Himalayan kingdom of Selgina. It will be his job to guard the incognito princess. She is due to succeed her late father to the throne, and it is feared that Red agents might try to assassinate her in order to sway Selgina towards communism.
On Princess Salno's plane, a bomb has been set by her aide Malness. The Princess sees a strange light pass the plane. A voice tells her to escape from the plane. Obediently, she opens the door and jumps. Immediately afterwards, the plane explodes.
In the mountains, Professor Murai leads a team to the gorge to examine the huge meteorite that crashed near Mt. Jiridaki. Hiking through the wilderness, they are shocked to find their compasses acting strange. The men finally reach the massive space rock. Professor Murai orders camp set up in the gorge. Suddenly, the meteorite exerts a magnetic surge, drawing the team's iron picks to it.
Back in Tokyo, Shindo is informed of the assassination of Princess Salno. He bemoans the death of such a beautiful girl for political reasons.
At her news agency, Naoko is told to go to central park where a prophetess has appeared and is drawing a huge crowd with her predictions. The prophetess claims to be from Mars, remaining serious, despite the harassing jeers of the crowd. She warns of the imminent destruction of Earth. The destruction will begin with a tragic accident in the Wazachin Mountains. Mt. Aso is again smoking, but scientists hold that this is normal, there is no danger, whatever prophecies have been made.
In Kurobe Gorge, the team is puzzled by the oddities of the meteorite. Some are even frightened by it. The rock seems to be growing larger and the magnetism comes and goes in erratic spurts.
Shindo returns home to his mother and sister. Naoko has been meeting with Professor Murai, interviewing him about the meteor. Shindo and their mother draw a different connection, however, and tease Naoko about a possible romantic interest in the geologist. During dinner, mother Shindo watches a television variety show, 'What are they doing now?' At the request of two young boys to see Mothra perform, the hosts provide the next best thing - the twin fairies. The Shobijin tell the boys that one Mothra is dead, but that the other one is fine, living on Infant Island. They agree to sing Mothra's song for the boys, and the television audience. As the show plays on TV, Shindo reads a newspaper, shocked when he sees a picture of the Martian prophetess. She looks exactly like Princess Salno!
Shindo points out the resemblance to Security Chief Okita. Okita agrees that it is an amazing likeness, but can't understand how she could have survived. There is a tradition that the Princess of Selgina always wears the royal bracelet, but she may have removed it to hide from her assassins. Shindo wants to pick her up, but Okita demurs that demagoguery is not a crime. He relents and tells Shindo he can follow it up, but strictly on his own.
In Selgina, the head of the conspiracy sees a Japanese newspaper with a picture of the prophetess. He demands to know if the plane blew up. Malness protests that the woman in the picture can't possibly be Salno. Malness is sent to Japan. He will find out if the woman is or is not Salno. If she is, he will finish the job and kill her. At the airport, Malness is met by a trio of Japanese thugs. They take the assassin to a hotel, from which they can base their operations.
Shindo stuns Okita by bringing him the royal bracelet. A fisherman was caught trying to pawn it. He says that it was given to him by a woman he found at sea, floating like a bit of cork. The woman traded the jewelry to him for his clothes. Asked why he didn't report the matter, the fisherman says that when he got to shore, the woman disappeared. He is shown a book of photos and identifies Princess Salno as the woman, the prophetess being the same woman wearing his clothes. Okita does not understand how Salno could have survived, but Shindo has talked with the UFO expert, who offers the implausible theory that she fell into a dimensional rift when the plane exploded.
Naoko tries to find the prophetess, meeting her brother on the street. They go to a bar for a drink, soon joined by Professor Murai who Naoko had been expecting. Murai is on his way back to Kurobe Gorge, still puzzled by the weirdness of the meteorite. A TV report interrupts the talk. The prophetess has appeared again, this time at Mt. Aso.
The prophetess warns the tourists at the volcano to leave immediately. It is not an eruption that threatens them, but the monster Rodan. One man's hat is blown off by a gale into the crater. Another onlooker offers to go down and retrieve it for the sum of 200 yen, ignoring the prophetess' warnings. He reaches the bottom just as the crater wall begins to crumble away. Rodan emerges from the volcanic rock, rising into the sky as terrified people flee.
In Tokyo Bay, the Shobijin are boarding a ship to return to Infant Island. The prophetess appears, warning that the ship must not sail. The captain angrily demands that she be put ashore. Naoko leads the woman away, offering to take care of her.
At the gorge, the team continues to puzzle over the meteorite's impossible growth. At the same time, the magnetism again manifests itself.
Naoko takes the Martian prophetess to a hotel to interview her. As fate would have it, it is the same hotel occupied by Malness and his thugs. The assassin sees the prophetess but is puzzled that she did not recognize him.
Naoko prepares to interview the prophetess, but is startled to learn that the Shobijin followed them. The fairies understood the prophecy and knew they could not sail on that ship.
At sea, the ship soon passes a school of frightened whales. High overhead, Rodan soars through the night sky. Rising from the sea is Godzilla. He at once blasts the ship with his atomic fire, igniting it.
In the hotel, Naoko gets the prophetess in some decent clothes. She offers to help the woman tell the entire country her warnings. A call from the front desk that Shindo has arrived causes Naoko to leave. Lurking in the hall, Malness and his gangsters seize the opportunity to break into the room. Downstairs, Shindo demands to know where the Princess is.
Malness interrogates the prophetess, determined to be certain if she is or is not Salno. He even threatens her with the knife he used to kill her father. He asks about the royal bracelet. The dazed prophetess admits that she had a bracelet, but that she gave it away. Malness is now certain that this is the Princess. Shindo forces Naoko to let him into the room. As the door opens, the fairies shout a warning and turn off the lights. A brief gun battle ensues, but Malness and his men escape from the balcony. The prophetess sits in the dark, calmly reading a book. Shindo decides to take the woman to a doctor for examination.
Tokyo hurriedly tries to evacuate as Godzilla comes ashore, crushing everything in his path. Rodan continues to circle overhead, seemingly stalking the other monster. Godzilla pursues the high-flying beast.
In Kurobe Gorge, the meteorite rumbles. Professor Murai and his team watch as the rock glows and then splits open. Fire and smoke spews from the ruptured rock. At last, there is a tremendous explosion. The fireball rises high into the air, the flames condensing into a hideous form, a winged three-headed dragon monster.
Shindo takes the prophetess to Dr. Tsukamoto who can find nothing physically wrong with her. The prophetess addresses the men, speaking of a monster named Ghidorah who wiped out all life on Mars millennia ago. She also says that Ghidorah has arrived on Earth.
Authorities try to evacuate cities in King Ghidorah's path. The space monster flies over the cities bringing death and destruction with the shockwaves from his supersonic flight.
Back at Dr. Tsukamoto's institute, Godzilla and Rodan are drawing closer. The two monsters engage in a running battle, Godzilla unable to come to grips with his flying foe.
At the Diet Building, Japanese leaders discuss how to deal with the monsters. Murai has brought the Shobijin to the meeting, saying that perhaps Mothra can help. The fairies are doubtful. Only by having Mothra convince Godzilla and Rodan to cooperate can King Ghidorah be stopped. It seems a ridiculous idea, but Ghidorah's appearance over Tokyo, ravaging the city with his gravity beams, makes everyone desperate enough to take the chance. The Shobijin call Mothra, summoning the caterpillar monster to Japan.
Meanwhile, Godzilla and Rodan continue to fight. Godzilla is frustrated when Rodan proves impervious to his atomic flame, laughing off the radioactive blasts.
As a result of the telecast Diet meeting, Malness learns that Salno is at Dr. Tsukamoto's institute. The advance of the monsters causes Dr. Tsukamoto to dismiss all non-essential personnel. Only himself and Shindo remain to attend to the prophetess. Dr. Tsukamoto intends to try shock treatment when hypnosis fails to break through to Princess Salno's personality. Shindo sets the generator, unaware that the assassins are observing him. Malness decides to let the doctor do his work for him, resetting the generator to deliver a lethal charge. Before the charge can be given, however, Rodan lifts Godzilla high into the air, dropping the monster on the power lines, plunging the institute into darkness.
A gun battle ensues when Shindo goes to check the power. Naoko, Murai and the Shobijin arrive. Murai comes to Shindo's aid and Malness is again forced to flee. The assassins again escape Shindo. With the monsters drawing closer, the heroes decide to leave the institute.
On a rocky cliff, Godzilla and Rodan face off. Neither monster is able to seriously harm the other, however. The battle is a complete stalemate. The windstorms generated by Rodan's wings keeps Godzilla at bay, but Godzilla is able to hurl boulders at his foe.
Refugees pack the roadways, forcing Shindo's group to abandon their car. They climb a hill and watch as Mothra arrives. Mothra crawls to where Godzilla and Rodan are fighting. Her cries go unnoticed until she sprays silk, first on Godzilla, then on Rodan. Amused, the two monsters briefly break off hostilities and converse with Mothra. The Shobijin telepathically interpret the conversation for their human companions. Godzilla and Rodan see no reason to help mankind and do not wish to help against Ghidorah.
The assassins force their car through the refugees. But just then, King Ghidorah arrives, blasting the mountainside and burying the road in rubble. Only Malness survives, badly injured by the avalanche. King Ghidorah lands, ravaging the villages and towns in his path.
The monsters continue to argue. At last, Mothra gives up. She will fight King Ghidorah on her own, despite the unevenness of the contest. Mothra crawls down to the village and is instantly battered by King Ghidorah's gravity beams. Godzilla then appears, charging down to attack the space monster. Rodan also circles overhead.
So intense is the spectacle of battle that no one notices when the prophetess wanders off. The group disperses to try and find the deluded Princess Salno.
King Ghidorah holds his own against Godzilla, but Rodan lures him away. Crashing into the pursuing King Ghidorah in mid-air, Rodan forces the space monster down on a rocky cliff. Godzilla and Mothra arrive to aid Rodan, Godzilla hurling boulders at Ghidorah.
The prophetess prays for aid against Ghidorah. Malness finds her and takes aim with a sniper rifle. But the assassin is injured and cannot aim very well. The shot only grazes Salno. She drops to a nearby outcropping. Shindo arrives, trading shots with Malness and climbs down to the stranded Salno. She again is herself and recognizes her attacker. Malness wounds Shindo and prepares to finish off both the Princess and the cop. A stray blast of King Ghidorah's gravity beams causes another avalanche, however, and Malness is killed by the resulting rockslide. The others arrive and rescue Shindo and Princess Salno from the ledge.
The battle with King Ghidorah progresses. Godzilla, Rodan and Mothra all pummel bite and claw the space monster. Rodan allows Mothra to climb onto his back, becoming a mobile platform from which Mothra can spray her silk onto King Ghidorah. Godzilla prevents King Ghidorah from eluding the attack, grasping his tails. Soon, King Ghidorah's heads are completely encased in silk, preventing him from using his gravity beams. Godzilla hurls the space monster off the cliff and King Ghidorah retreats, flying skyward, back into outer space.
Princess Salno, now herself, marvels at her ability for prophecy and claims of being a Martian. The trauma of her injury brought her back. She thanks Shindo for saving her life so many times. She is now returning to Selgina.
Elsewhere, the Shobijin and Mothra are also returning to their home, wishing farewell to Godzilla and Rodan, who watch Mothra swim away from a seaside cliff.