A spaceship, the P-1, is launched by the World Space Authority to investigate a mysterious planet discovered just beyond Jupiter. On board are astronauts Glenn and Fuji. They radio back to Earth and the WSA. They are on course for Planet X. Dr Sakurai asks the men how they are holding up. Fuji asks about his sister, worried that she might marry while he is away from Earth. His sister, Haruno, resents the intrusion.
Elsewhere, Haruno's boyfriend, an inventor named Terry Tetsuo, tests his new invention, a small loud alarm device he calls the Ladybird. Tetsuo is surprised by a phone call, someone offering him a contract for the Ladybird. Back at the WSA, Dr Sakurai answers the questions of reporters about Planet X and why it had not been discovered until recently. It is a dark world, found only due to radio waves emanating from there. Dr Sakurai would rather not speculate on whether the radio signals are the work of an alien intelligence.
In a lush restaurant, Tetsuo celebrates his sale with Haruno. A toy manufacturer is buying the device. Ms Namikawa of the World Education Corporation arrives with Tetsuo's contract, saying he will be paid for his device when it is marketed. Ms Namikawa recognizes Haruno as Fuji's sister, saying the WEC is very interested in the WSA and the space mission. Haruno wonders why the WEC is paying Tetsuo so much for his invention.
The P-1 makes its approach to Planet X. Now on the blind side of Jupiter, the ship comes out of radio contact. Planet X displays an unusually warm temperature for a planet so far from the sun. The P-1 lands, and Glenn and Fuji set foot on the desolate, rocky alien world. As the astronauts begin to explore, Fuji leaves Glenn to set up a tele-meter, while he goes to plant the flag on a ridge. A sudden burst of thunder and lightning alarms the men, but Fuji proceeds, discovering footprints in the dusty soil. He radios back to Glenn to warn him, but receives no answer.
Hurrying back, Fuji finds not only Glenn missing, but the P-1 as well. A strange lighted elevator rises from the soil, a voice ordering Fuji to enter the cylinder. The voice says that it is the Controller of Planet X. When Fuji refuses to obey, the Controller forces him to comply, a laser shooting from the cylinder and knocking Fuji's gun from his hand. Fuji obeys, and the Controller tells him that he already has Glenn and the ship.
Fuji finds himself in an underground complex. The voice of the Controller guides him through the vast system of tunnels, leading Fuji to a room in which he finds Glenn seated. Glenn is unharmed. The lights in the room rise and the Controller and several of his men enter. They look human, though their grab is strange and alien. The Controller asks that the two men sit and make themsleves comfortable.
The Controller wants to discuss an important matter with the astronauts. The P-1 is safe, revealed in a hangar by a video screen behind the Controller. Just then, alarms sound. Monster Zero has arrived. The Controller explains that Monster Zero is the demon of the galaxy and the reason why his people can no longer live on the surface. The Controller shows his guests Monster Zero on the view screen. They are stunned to learn that Monster Zero is King Ghidorah!
The Controller has been unable to drive King Ghidorah away. All Planet X can do is wait for King Ghidorah to go away on his own. The monster ravages the surface with his gravity bolts, causing cave-ins. At one point, a hydrogen-oxide plant is damaged. The Controller quickly leaves to investigate, leaving Glenn and Fuji trapped in a forcefield until he returns. The astronauts ponder this, realizing that water must be very valuable on Planet X, and that the Controller does not wish outsiders to know about this deficiency.
The Controller returns, announcing that Monster Zero has left and that they are all safe now. He goes on to say that Planet X needs an exterminator, a way to get rid of Monster Zero. He wants to borrow from the Earth the monsters Zero-One and Zero-Two - Godzilla and Rodan. Once again, Glenn and Fuji are stunned. The Controller wants their help, he knows where Godzilla and Rodan are located, he merely asks permission to capture and transport them. In return, he offers a miracle drug that will cure all disease.
The astronauts leave in the P-1, bearing the Controller's message back to Earth. The Controller wishes them a safe journey. The P-1's return causes a great sensation. World leaders debate Planet X's proposal. The friendship of Planet X is greatly welcomed, and the miracle drug is eagerly anticipated. The council decides that they will order full cooperation with Planet X if Godzilla and Rodan are indeed found where the Controller said they would be. JSDF search teams quickly scatter to search Lake Myojin for Godzilla and Mt. Washigasawa for Rodan.
At the same time, Tetsuo tries to see Ms Namikawa at the WEC offices, wondering when his invention is going to be marketed and he will be paid. He is given the brush off by a WEC employee. The employee returns to his boss, who is a Planet X operative. The boss tells him to get rid of Tetsuo. As for the invention, the alien burns the blueprints to the Ladybird alarm.
Haruno leads Tetsuo to a luncheon with Glenn and Fuji, something Tetsuo is very nervous about. At the restaurant, Glenn tells Fuji about his new girlfriend. The conversation turns back to Planet X, and their water supply concerns, and how far the Controller can be trusted. Haruno and Tetsuo arrive. Fuji is opposed to the courtship, wondering how Tetsuo will be able to support his sister. Glenn is more sympathetic. He leaves to go on his date, Haruno and Tetsuo are surprised to see him drive off with Ms Namikawa.
At Lake Myojin, the searchers discover radiation from Godzilla. The news spreads like wildfire. It is certain that Rodan will also be found where the aliens have said. Glenn arrives at the WSA to collect Fuji. They drive toward Lake Myojin. Glenn says he went to a bungalow here with Ms Namikawa. He also says that he thinks he saw the Controller. Waking in the middle of the night, he saw the Controller in his room, and that the alien said something about all preparations being made. The girl, of course, said she had seen nothing. Again, the astronauts wonder if Planet X can be trusted.
As the astronauts drive to inspect the bungalow, they see that the area is cordoned off. A strange glow has appeared in the lake. Instead of Godzilla, however, an alien saucer rises from the lake, followed by two others. The aliens didn't wait for permission, they were already on Earth.
The next day, one of the saucers lands and top officials meet with the Controller as he emerges from the ship. He again expresses his hopes of peace and harmony between their two worlds. He claims that the early arrival was out of concern for the Earth. Any further delay and Godzilla would have awakened, causing much destruction.
The Controller sends one saucer to Mt. Washigasawa while another fires a beam into Lake Myojin. Godzilla's body levitates from the water and the sleeping monster is encapsulated in an energy bubble. The other saucer fires a laser into the side of Mt. Washigasawa and removes the sleeping Rodan in like fashion.
Glenn, Fuji and Dr Sakurai depart with the Controller on his saucer. Glenn makes a tense departure from Ms Namikawa who asks him to marry her and not leave. Tetsuo follows Ms Namikawa as she leaves. With the two monsters in tow, the trio of saucers depart. Dr Sakurai is amazed by the streamlined control room. The Controller feeds his will into the computer with brain waves and controls the ship in this fashion. They can do the same with plants and animals. At an amazing speed, the saucers travel back to Planet X.
Meanwhile, Tetsuo follows Ms Namikawa to an island house. Ms Namikawa receives a reprimand from her superior, the head Planet X agent. Tetsuo emerges from hiding, but is discovered on the island. The inventor is soon captured by means of a trap door.
The saucers arive on Planet X. Releasing the monsters from the tow beams, teams of X-Seijin try to reclaim the water from the energy bubbles that hold Godzilla and Rodan. The work is interrupted, however, when Monster Zero arrives, forcing the aliens to retreat back underground.
Godzilla and Rodan revive and at once join battle against King Ghidorah. After a surprisingly quick fight, Monster Zero is driven off. The Controller is very pleased, it is the first time Planet X has driven off Monster Zero without suffering any damage. He is less pleased, however, when he discovers that Glenn and Fuji are gone from the command room.
Glenn and Fuji prowl the complex, trying to find anything of informative value. Trying to escape guards, they stumble on a natural cavern ridden with gold. They also find women who look exactly like Ms Namikawa. The astronauts are then caught by guards and taken back to the Controller. The Controller interrogates them, asking if they learned anything. Fuji replies that they discovered that water is more valuable than gold on Planet X, but the Controller rebuffs him, saying that water is not a scarcity on Planet X. Glenn also wonders why the women all look alike, though the Controller lecherously mentions that he thought the astronaut would find the women most appealing. The Controller forgives the two men for their indiscretion and presents Dr Sakurai with a taped recording of the formula for the miracle drug he promised the people of Earth. An exact copy of the P-1, built by the computers of Planet X after examining the original, stands by to take the men back to their planet.
Godzilla and Rodan seem to resent being left behind. The duplicate P1 speeds off, leaving the two monsters on Planet X.
Haruno goes to the World Education Corporation and sees Ms Namikawa, asking about Tetsuo. Namikawa says that she hasn't seen him for quite some time. Elsewhere, Tetsuo is kept in a cell at the alien base. The Controller contacts the alien agents, telling them to start implementing their plans. The agents watch with interest as the P-1 facsimile lands at the WSA facility.
The world watches as Dr Sakurai presents the tape at the WSA. The tape is played, but soon it becomes apparent that the tape is not a formula but an ultimatum from Planet X's Controller. Earth will submit to his rule and become a colony of Planet X. Failure to do so will result in the destruction of Earth. The news sets off demonstrations across the globe. Some wish to capitulate, but most of the world wants to resist the aliens. Riots break out as the factions clash.
Amidst the turmoil, Glenn comes upon Ms Namikawa at the looted WEC building. She is dressed in the garb of Planet X now. Once again, she begs Glenn to join her, as a citizen of Planet X he would be able to marry her. Glenn refuses to betray Earth. The other WEC Planet X agents arrive, seizing them both. The colonial commander declares that Ms Namikawa is a traitor. She embraces Glenn quickly before the commander destroys her with a disintegrator pistol, the computer controlled spymaster disgusted by her display of emotion. Glenn is led away by the aliens.
At the WSA, Dr Sakurai reports that King Ghidorah is in the USA. The military wants to use nuclear weapons against the aliens and resist to the last. Alien saucers devastate the WSA facility, destroying the P-1. The Controller takes the silence of world leaders as a refusal and announces that they will conquer the Earth. King Ghidorah is stationed in the western hemisphere, controlled by magnetic waves from their computers. Dr Sakurai observes that King Ghidorah was always one of their weapons. The Controller also manipulates Godzilla and Rodan with the same method. He gives 24 hours for the Earth to capitulate before unleashing the monsters to destroy the Earth cities.
Dr Sakurai wonders about the magnetic waves used to control the monsters, showing Fuji a report about A-Cycle waves and their disruptive effect on magnetic waves.
Back at the alien base, Glenn is thrown into the same cell the aliens are holding Tetsuo in. Glenn wonders why the cell has been soundproofed. Elsewhere, the colonial commander tells his men that they will be in charge of mop up duties. No humans are to survive.
At a meeting of national leaders, the military again presses for the use of nuclear weapons. Dr Sakurai proposes a plan to sever the magnetic waves controlling Godzilla and Rodan. Already Fuji and other WSA scientists are hard at work on the problem. Dr Sakurai leads the council to the test lab. Fuji demonstrates the A-Cycle waves blocking magnetic waves. The problem is discovering the lengths and frequencies of the waves the aliens are using. Dr Sakurai proposes a laser effect that concentrates on the upper and lower frequencies. If it doesn't work, they won't get a second chance to try again.
The Controller readies his forces. Meanwhile, Glenn and Tetsuo ponder their situation. Tetsuo finds a note in Glenn's jacket from Ms Namikawa. It says that the people of Planet X are controlled by their computers, and that a simple sound can destroy those computers. Tetsuo realizes that is why they bought his invention. He even has the prototype alarm with him. Using the device, they subdue their guards, who cannot bear the sound, and escape their cell. The colonial commander discovers the escape, destroying the island's supply boat as it leaves. However, Tetsuo and Glenn are not on the boat, they are swimming across the lake.
Glenn and Tetsuo arrive at the WSA where Fuji has solved the problem with the A-Cycle waves. News of the alarm sound and its effect on the aliens is instantly implemented, as transmitting and reproduction facilities are hastily arranged.
The Controller changes plans and sends Godzilla and Rodan on the attack ahead of schedule. JSDF forces move to intercept the monsters, but already they attack the outskirts of the city. The A-Cycle projectors are moved by truck convoy towards Godzilla and Rodan and the saucers controlling them. The saucers add their deadly energy beams to the monsters' assault, targeting the truck convoy.
Fuji reports the disaster to Glenn and Tetsuo, who are almost ready to transmit the alarm sound. The Controller orders King Ghidorah to join the attack in Japan. Fuji has the second wave of trucks held back within the safety of a tunnel. The monster assault moves onward into the city, King Ghidorah, Godzilla, and Rodan wrecking a terrible toll and resisting JSDF efforts to repel them.
The sound of the Ladybird alarm is broadcast over national radio, so that every transmitter in the country can play it. The noise has its effect, disrupting the computers on the alien saucers and disorienting the aliens. The truck convoy moves out, now safe from the saucers. The A-Cycle projectors fire, severing the controlling magnetic waves. Glenn supervises the military attack on the alien base he and Tetsuo escaped from. The disabled aliens are unable to resist, or heed the Controller's demands for them to adjust the computers.
Godzilla and the other monsters are stunned when the control waves are severed, lying immobile. The saucers continue to flounder, unable to be controlled. The earth base is destroyed by tank shelling. His conquest crumbling on all fronts, the Controller refuses to retreat. Instead, he orders his people to escape by self-destructing their own saucers and passing into the dimension beyond death.
Free of alien control, the monsters revive. Godzilla and Rodan attack King Ghidorah, knowing their old enemy. The trio grapple, falling over a cliff, all three disappearing in the sea. It is King Ghidorah who emerges, flying back into outer space. Haruno wonders if King Ghidorah killed Rodan and Godzilla, but tetsuo doesn't think so, Rodan and Godzilla are too tough. Fuji laughs, at last accepting Tetsuo as his future brother. Dr Sajurai interrupts, telling Glenn that he will be flying back to Planet X as Earth's first ambassador.