At a festival in a village near Mt. Fuji, Shoji Atsumi, his sister Hiroko and his girlfriend Mitsuko meet with Ryochi Shiraishi. Despite the happy atmosphere, Ryochi displays no interest in the festivities, even neglecting to dance with Hiroko, his fiancée. Atsumi follows the moody Ryochi, telling him that everyone is concerned about his sudden change in behavior. Atsumi wonders why Ryochi, a physical astronomer, has taken up residence in a small village.

Suddenly, the nearby forest erupts into flames. Ryochi runs toward the fire. He warns some of the villagers against trying to fight the fire. The men ignore him, determined to save the trees. They are horrified to find that the trees are burning from their roots up, the source of the flame being underground. The flames soon surround the doomed men.

At the astronomical observatory Atsumi reports to Dr. Kenjiro Adachi, presenting him with Ryochi's thesis - a study of Mysteroid - a planet destroyed long ago which once existed between Mars and Jupiter. Ryochi states that the planet he has christened Mysteroid - 'Star of Mystery' - now exists only as a ring of asteroids. Dr. Adachi observes that the thesis is incomplete, very unlike Ryochi to turn in an unfinished work.

A phone call interrupts the discussion. Atsumi takes the call, being told that a landslide has leveled the village Ryochi was living in. Atsumi goes with police to investigate the incident. The entire village has been destroyed, with no survivors and radiation has begun killing fish in the nearby streams and creeks. The radiation puts an even more sinister aspect on the destruction. Even more puzzling is the sudden dissipation of the radiation.

Investigating the scorched region of the forest fire, Atsumi and the police watch in horror as an enormous metal beast emerges from the mountainside. The men barely escape the monster with their lives, Moguera's heat beams destroying their jeep.

Atsumi and the surviving police make their report in the city to scientists and officials. News arrives that Moguera is attacking the power plant. The alarm is given, and the city is evacuated as Moguera continues to stalk unhindered, blasting buildings with its heat ray and setting entire streets on fire. At last, Defense Forces arrive, deploying just outside of the city. The fleeing civilians are urged to cross a large railroad bridge, marking the JSDF's line of defense.

Moguera wades through the hail of machine-gun fire, rockets, bazookas, mortars and flame-throwers. As Atsumi and Mitsuko flee, they see three sinister lights speed across the sky, heading toward Mt. Fuji. Moguera at last sets foot on the railroad bridge, trying to reach the JSDF troops. The bridge has been set with explosives and is detonated when the monster sets foot on it. When the smoke clears, the destroyed robot lies in the midst of the wreckage.

In the Diet, Atsumi addresses Parliament and assembled scientists and JSDF officers. He says that the fire and Moguera were the work of some intelligence. Analysis of the robot reveals that it is made of some chemical substance with ingredients unknown to man. Who made the machine and for what purpose is unknown.

At the observatory, Dr. Adachi notes sinister lights emerging from behind the moon and descending toward Earth. It is exactly as stated in Ryochi's thesis. Atsumi tells Dr. Adachi that he saw similar lights during Moguera's attack. Dr. Adachi announces the UFOs to the world and an expedition is sent to a lake mentioned in Ryochi's report. Suddenly, a massive plume of dust shoots from the ground. Soon, a huge dome emerges from beneath the earth.

A voice addresses the shocked men, claiming it means them no harm. The voice says that they wish to negotiate with five of the scientists who are present, including Dr. Adachi and Atsumi. The selected men advance toward the dome while the JSDF mobilizes to react if the aliens prove hostile.

The men enter the dome and meet with the human-like aliens. They are Mysterians, survivors of the nuclear war that destroyed the planet Mysteroid. The Mysterian commander condemns the fact that the Earthlings are mobilizing their weapons against the aliens. He explains that some of their ancestors escaped Mysteroid to settle on Mars. He further states that they are ruled by science - which recognizes no boundaries, racial, national, or planetary. He hopes that the Earth will not attack them, as they will reply in kind.

The Mysterians request only 3 km of land for peaceful purposes of scientific study and as a base for further space exploration. Also, due to Strontium 90 poisoning in their race, they require new breeding stock and wish to inter-marry with Earth women. They have already secured three of the individuals they have chosen from the destroyed village. Both Mitsuko and Hiroko are among the others selected. His demands made, the Mysterian commander dismisses the scientists.

It is decided that the Mysterians are not to be trusted, having taken what they want before asking. Although the Mysterians may be too powerful to defeat, it is decided to resist them at all costs. Army forces deploy around the Mysterian base.

Atsumi tells Mitsuko and Hiroko about the Mysterian demands. Soldiers have been assigned to protect the two women. Ryochi's voice confirms Atsumi's story. The scientist is revealed on the TV, transmitting from the Mysterian base. He has joined with the aliens. He warns that the JSDF must not attack, it would be disastrous. Ryochi claims that he is only serving science by helping the Mysterians. To contact him again, Atsumi has only to turn on the TV.

At defense headquarters, Atsumi tells Dr. Adachi about Ryochi's defection. It is too late, however, to stop the attack.

The JSDF launches an all out assault on the Mysterian dome. Tanks, cannons and missiles cannot penetrate the Mysterians' force shield and the Mysterians employ a powerful gamma ray to knock JSDF fighters from the sky and melt the ground forces with intense heat. Mysterian saucers also aid in the defense of their base, easily besting the slower Earth aircraft. Tanks which draw too close to the dome are sucked underground by the Mysterians' powerful digging machines. The JSDF forces are soundly defeated.

Mysterian saucers fly over Japan's cities, announcing their peaceful propaganda to the Japanese citizens. Meanwhile, the military plans its next course of action. An electronic cannon is put into production. At a press conference, Dr. Adachi stresses that the nations of the world must unite against the Mysterians. What is happening in Japan will all too soon be happening in the United States and Soviet Union. If the Mysterians gain their foothold on Earth, they will begin arriving in great numbers.

In the Mysterian base, Ryochi is shown the complete plan for the underground fortress the aliens are building. 500 hours will see it completed and then all of eastern Japan will be under Mysterian control.

Japanese leaders meet with delegates from the US and USSR. The Americans have launched a satellite from Arizona to watch and monitor the Mysterians' activities in space. Atsumi lets the men talk with Ryochi through the TV. Ryochi tells the men that the Mysterians are only preventing mankind from destroying himself and the world - repeating the tragedy of Mysteroid. Earth cannot be left in the control of humans. After all, Ryochi says, it is not man or Mysterian who truly rules, but science itself.

The traitor's words make the governments of Earth determined to cooperate and destroy the Mysterians. The UN forces discuss the weaknesses of their enemy. Atsumi joins ground observers to watch the new attack on the Mysterian dome. The UN deploys a pair of super-aircraft, the Alpha and the Beta I to attack the dome. The aircraft are unable to harm either the saucers or the Mysterian dome with their rockets and guns. At last, the Beta I gets too close and the gamma ray from the dome destroys the aircraft. The Alpha beats a hasty retreat.

Atsumi and some of the observers emerge from the bunker and witness firsthand the defeat. Atsumi discovers an underground tunnel, but it is too dangerous to investigate at present.

The electronic cannon is rushed through production. Meanwhile, the Mysterians announce that they now control 120 km and will not abide intruders in their area of control. US representatives suggest using nuclear bombs on the Mysterians, but a dour Dr. Adachi advises against repeating the tragedy of Mysteroid. An American scientist enters the conference, telling everyone that the US has developed a weapon called a Markalite which can reflect the Mysterians' ray back at them while firing its own destructive beam. Its range is limited, presenting the problem of how to deploy the Markalites. The weapons arrive from the US and are hastily assembled.

Meanwhile, a Mysterian saucer hovers above Atsumi's home. The aliens descend and abduct Mitsuko and Hiroko before anyone is aware of their arrival. Atsumi watches helplessly as the saucer speeds away.

It is decided that the attack must be started, with or without the electronic cannon, if only to delay the construction of the Mysterians' base. The countryside is evacuated. Atsumi decides that he will try and enter the base through the tunnel he discovered and rescue the kidnapped women, despite the coming attack.

Rockets carry the Markalites within range of the Mysterian dome. The weapons descend by jets to the Fuji plain. The Mysterians open fire on the two Markalites, only to have their own ray fired back at them. Meanwhile, Atsumi infiltrates the base from below. At the same time, Ryochi gathers the captured women together.

The Mysterians are unable to harm the Markalites, but at the same time the Markalites are unable to deal the dome any serious damage on their own. The weapons will falter soon, being able to handle the enormous amounts of energy for only a short time. As an act of retaliation, the Mysterians cause the lake to escape its banks and flood the countryside, laying waste to several towns and villages. As the aliens gloat at the destruction, Atsumi attacks their power generators. He is quickly subdued and handed over to a Mysterian leader.

The Beta II is finally armed with the electronic cannon and sent into battle. In the Mysterian base, the Mysterian officer leads Atsumi to the Earth women. The Mysterian is actually Ryochi. Ryochi tells Atsumi and the women to escape; there will be an explosion soon. He gives Atsumi the rest of his report on the planet Mysteroid. The Mysterians have betrayed him. They want to rule not for the sake of science, but out of a lust for power. Ryochi heads back into the base to destroy it.

The combined power of the electronic cannon and the Markalites begins to effect the dome, while Ryochi finishes Atsumi's sabotage of the power room. The gamma ray is disabled and the Mysterian leaders decide to retreat back to their moon base. The underground fortress explodes in a brilliant fireball. The Beta II pursues the fleeing Mysterian saucers, but some of them escape back into space. As Dr. Adachi notes, the threat of the Mysterians remains and the nations of the Earth will have to remain united to guard against their return.