Astrophysicist Ryoichi Shiraishi, his fiancée Hiroko Iwamoto, his sister Etsuko, and his friend Joji Atsumi attend a bon festival in a village at the foot of Mount Fuji. During the festival, Shiraishi rushes out to investigate a sudden forest fire that has flared up nearby and he disappears during the confusion. The next day, Atsumi meets his mentor, Dr. Tanjiro Adachi, the head astronomer at the local observatory. Adachi hands him an incomplete report written by Shiraishi regarding a newly discovered asteroid he believed was once a planet between Mars and Jupiter, dubbed "Mysteroid". However, Adachi repudiates his radical theory.
Meanwhile, the village where the festival was held is completely wiped out by a massive earthquake. While investigating the area, Atsumi and a group of police officers stumble upon a giant robot, Moguera, which bursts from the side of a hill. It emits rays that destroy most of the investigation team; only Atsumi and the lead policeman survive. The robot then advances to a town near Koyama Bridge and met by heavy resistance from the Japan Self-Defense Forces. However, their artillery has no effect on Moguera, and the robot continues its rampage until it is destroyed by explosives detonated by the military near the Koyama Bridge.
After Atsumi briefs officials on what has been learned about the robot at the National Diet Building, astronomers witness activity in outer space around the Moon. They alert the world to this discovery; soon after, a gigantic dome emerges from the ground near Mt. Fuji. Dr. Adachi and five other scientists agree to hold a conference in the dome after a mysterious voice asks them to do so during an observation of the dome by a military and scientific entourage. The men are formally ushered into the dome, where a scientifically advanced humanoid alien race known as the "Mysterians", reveal their demands from the people of Earth: a two-mile-radius strip of land and the right to marry women of Earth. The Mysterian Leader reveals that thousands of years ago their planet—Mysteroid, once the fifth planet from the sun—was destroyed by a nuclear war. Although some Mysterians were able to escape to Mars before their planet was rendered uninhabitable, strontium-90 left the aliens' population deformed and they thus desire to interbreed with women on Earth to produce healthier offspring and keep their race alive.
Japan quickly dismisses their requests and begins the mobilization of its armed forces around Mount Fuji. Shiraishi—who vanished during the forest fire—reveals that he has sided with the Mysterians for their technological achievements. Without hesitation, Japan quickly launches a full-scale attack against the Mysterians' dome, but their modern weaponry is no match for the Mysterians' technology. This setback causes Japan to plead with other nations to join forces in eradicating the Mysterians threat. The nations around the world respond and issue another raid on the Mysterians' dome, which also fail despite deploying newly developed airships.
The Mysterians then increase their demand, asking for a 75-mile-radius of land. The humans develop a new weapon, the Markalite FAHP (Flying Atomic Heat Projector), a gigantic lens that can reflect the Mysterians' weaponry. Meanwhile, the Mysterians kidnap Etsuko and Hiroko, causing Atsumi to search for them and locate a cave entrance to a tunnel under the Mysterians' dome.
In the meantime, several Markalite FAHPs are deployed, and the final battle against the Mysterians' base of operations commences. Atsumi enters the dome and finds the women kidnapped by the Mysterians, alive and unharmed in an unguarded room. He takes them back to the tunnel, where he finds Shiraishi, who admits the Mysterians deceived him and truly have no good intentions. In a final attack on the base from the inside, Shiraishi sacrifices himself while the Markalite FAHP continue their assault. In the midst of the battle, a second Moguera deployed by the Mysterians is disabled after one of the FAHPs falls on top of it. As Adachi and the women reach safety in the hills above the Mysterians' occupied land, the dome collapses and explodes. While some of the surviving Mysterians flee into space in their spaceships, Dr. Adachi comments on the need for continued vigilance.
Earth's nations unite to launch major attacks on the Mysterians' dome after rejecting the aliens' demands. The film ends as humanity confronts the advanced technology of the invaders in a climactic battle.
The climax of The Mysterians sees previously divided nations joining forces against a technologically superior extraterrestrial threat. This ending underscores themes of unity and resilience in the face of overwhelming odds, as well as humanity’s refusal to submit to coercive alien demands. The struggle against the Mysterians highlights both the geopolitical anxieties of the 1950s and a hopeful faith in international cooperation.