Eight months since Godzilla retrieved his Queen's egg.
During an unseasonably warm winter night, a reporter named Naoko Shindo observed members of a UFO club searching the sky for flying saucers.
When they fail to spot a UFO, the head member believes that the aliens won't reveal themselves because they brought a nonbeliever into their midst.
Naoko ask "do you actually believe aliens exist?"
The head of the club members replies "there have been strange phenomenons occurring across the globe, such as warm temperatures in winter months."
Naoko ask "do you think the world would explode?"
The leader replies "I feel something terrible will happen soon."
Soon a huge meteor shower falls over Japan, with one particularly large meteor crashing in the Kurobe valley.
Meanwhile, Naoko's brother, Detective Shindo, is given an assignment by his chief of police.
Shindo is assigned to act as a bodyguard for Princess Maas Doulina Salno, ruler of a small Himalayan kingdom of Selgina, who will be visiting Japan to escape political opposition in her home country.
While Princess Salno's plane is flying over Japan, she suddenly becomes possessed by a mysterious voice, who orders her to jump out of the plane immediately just before it is blown up by a bomb.
Professor Murai and his team arrive near Kurobe Dam and are assigned to study the meteor that crashed in the Kurobe valley.
As they approach the meteorite, they find all their compasses are all malfunctioning.
Once they reach the meteor, they discover that it is emitting a powerful magnetic force.
On Infant Island, Godzilla woke up sensing a threat and his fins began giving off an imtimidation light show.
Mothra sense it too and chirps "do you sense it too?"Godzilla growls "yes, a big threat against this world."Mothra chirps "we better go investigate it."
Godzilla and Mothra leave Infant Island and travel to Japan to investigate the disturbance.
At Kurobe Dam, Professor Murai and his team immediately begin studying the strange meteor, when it starts slowly growing in size.
Elsewhere in Japan, a mysterious woman appears and begins offering predictions for the future.
Naoko is sent to cover the prophetess, and attempts to get an interview with her.
Naoko ask her "where are you from?"
The prophetess replies hail Venus" and says "terrible disasters will begin to happen starting at Mount Aso."
Detective Shindo sees a picture of prophetess, and notice that she bears a strong resemblance to the Princess, and ask his chief to allow him to pursue the case.
In Selgina, the head of the political opposition learns that a woman strongly resembling the Princess has been seen in Japan.
He orders an assassin named, Malmess, who had previously killed Princess Salno's father, to travel to Japan and kill the Princess or be killed himself.
Detective Shindo searches for leads on finding the prophetess and encounters his sister, who is also looking for the prophetess.
The two of them go to a bar to meet with Murai, who is telling Naoko a story about the meteor in Kurobe.
Soon they see a news report on television showing the prophetess speaking at Mt. Aso.
She warns the surrounding crowds, that the volcanic gasses inside the mountain will resurrect Rodan, but her warnings are laughed at by the crowd.
Suddenly Rodan emerges from the crater after eight years of hibernation and takes flight.
Rodan resumes his reign of terror across Japan.
Then the Venusian reappears at the port and tells the captain of a cruise ship "you can't sail out to sea because two monsters are coming."
Two Shobijin girls become intrigued by the Venusian.
Naoko arrives at the scene and convince her to come with him to a hotel so she can do a story on her.
Malmess and his men follow them to the hotel and enters the room after Naoko leaves.
Malmess puts a knife to the prophetess' throat to threaten her.
Detective Shindo arrives at the hotel to try and secure the prophetess, believing her to be the Princess.
When he enters the room, the Shobijin girls kill the lights and say "there are killers in the room.
Shindo opens fire and chases the assassins off.
Once the lights are turned back on, he finds the prophetess meditating in a corner.
Naoko ask the Shobijin girls "why are you girls here?"
The Shobijin girls reply "we came to warn you that Godzilla and Mothra are on their way here."
Soon the captain of the cruise ship radio in that Godzilla is coming towards Japan with a worm.
Godzilla and Mothra comes ashore in Yokohama and Godzilla's attention is caught by Rodan flying overhead.
Godzilla and Mothra follow Rodan to Mt. Fuji area, where they begin a conversation.
Detective Shindo brings the prophetess to the laboratory of Dr. Tskukamoto who attempts to diagnose whatever mental illness affecting her.
The doctor fails to help her.
The prophetess tells them "a thousands of years ago, Venus was home to a great civilization far more advanced than Earth's. An evil space monster named King Ghidorah arrived on the planet and completely annihilated the planet.
The few that survived fled to Earth and assimilated into the planet's civilization and lost their identity."
Detective Shindo curious ask "who is King Ghidorah?"
The prophetess replies "I'm the last descendants of the Venusian refugees and King Ghidorah has already arrived on Earth."
In Kurobe, Murai and his men notice that the meteor's magnetism has seemingly stopped.
They go to sleep, and the meteor splits open and begins shooting out sparks.
Murai holds up a Geiger counter which registers a strong radioactive reading.
Soon a pillar of flames blast from the meteor into the sky, where it materializes into King Ghidorah, a three headed golden dragon.
King Ghidorah flies over Japan, blasting cities with his gravity beams.
The government convenes a meeting on how to deal with King Ghidorah, Godzilla, Rodan and Mothra.
King Ghidorah lands in Tokyo and roars "who dares to challenge me?!"
Godzilla, Mothra and Rodan head to Tokyo to face the challenge roar.
Malmess and his men fail to kill the Princess resulting in his death.
Godzilla tells Rodan to help throw rocks at King Ghidorah while Mothra covers Ghidorah in her silk.
They proceed to defeat King Ghidorah.
After King Ghidorah is covered in silk, he flees into space.
Godzilla and Mothra head back to Infant Island.
Rodan went to an island and buried himself in the ground.
Elsewhere, someone drew a picture of King Ghidorah and a painting of Godzilla fighting King Ghidorah.