Thousands of years ago, a peaceful alien race lived on an asteroid between Mars and Jupiter. They were far more scientifically advanced than the beings of Earth. When Earth entered the Neolithic Age, this alien race had discovered the atom bomb. Despite all this progress, their world was devastated by terrible weapons when war erupted among their people. The bodies of those who survived were mutated and contaminated with Strontium-90, and following this catastrophe, the survivors moved to Mars. However, since that planet was such a wasteland, they had to find a new home that could fit all of their needs. They desired Earth...

Hiding on the dark side of the moon, these people planned their invasion for years. Finally, in the Earth year 1957, they found a place where they could begin their attack: Japan. The aliens arrived on Earth undetected, by transporting their UFOs from their mother ship and hiding underground in the Mt. Fuji area. A scientist by the name of Ryoichi Shiraishi however, discovered the race of extra-terrestrials. Instead of informing the authorities, he began to collect research on this remarkable discovery. He called their former home planet Mysteroid, a combination of the words "mystery" and "asteroid", and the aliens were dubbed "Mysterians". He transferred his reports to Dr. Adachi frequently; however, the doctor didn't realize that the species actually existed...

One summer night, the Mysterians finally set their plan into motion. They set a celebrating village aflame by heating the ground with terrific amounts of radiation. That same night, Ryoichi vanished without a trace. The next day, another village was destroyed when the ground caved in; everyone was killed. Not even a dog survived. When local officials investigated, they encountered something frightening: a huge, burrowing robot armed with powerful lasers: Moguera. That night, the monstrous mech attacked another village, where it was met with resistance. The bridge leading out of the village was destroyed, ending the robot's destructive force. Suspicions started to rise when it was discovered that the substances that comprised Moguera were not of this Earth.

Meanwhile, Dr. Adachi witnessed the UFOs soaring from behind the moon through his telescope, giving further proof that aliens were invading the planet, and prompting the scientist to announce his discovery. The following day, investigations were made near a local lake, when something startling happened. A dome appeared from beneath the ground, another sign of the impending invasion. The visitors from space requested the presence of scientists, so the two races could work out a peace treaty. The aliens revealed their past, and informed the Earthlings that they were indeed the Mysterians whom Ryoichi had mentioned. Their only demands were a three-kilometer strip of land and the right to marry Earth women. One of the scientists, Joji Atsumi, was outraged when he discovered that both his sister and girlfriend were part of the first selected few.

After the meeting, the scientists agreed to declare war on the Mysterians, upon coming to the realization that they had already kidnapped a few of the Earth women whom they desired. When the military began the attack however, they were mostly destroyed by the defenses near the Mysterian Dome. The extra-terrestrial race flew around Tokyo, claiming they wished to avert war, but warned that they would retaliate if they are threatened. The United Nations came to an agreement; they would have to work together to defeat these aggressors. They built two ships known as BETA-Class Aerial Battleships, which were resistant to heat rays. The second assault against the Mysterians began. When one of the ships was annihilated by the overwhelming firepower of the Mysterians' arsenal, another blow was dealt to humankind. Following this tragedy, the Mysterians upped their request to ten kilometers of land, stating that if anyone were to enter the vicinity, they would surely be decimated. Ryoichi, who had willfully assimilated to the Mysterians due to allure of their advanced technologies, soon discovered that these people actually wished to rule the entire Earth.

Meanwhile, the Mysterians kidnapped Joji's girlfriend and sister, and in response, he decided to infiltrate the dome by himself. Finally, the humans enhanced the surviving BETA Class ships with electron guns, so their firepower would be at an ample strength to weaken the dome. This assault would work in conjunction with the arrival of powerful atomic heat rays, known as the Markalite Cannons. With a new plan of action finally concocted, the final assault began. As the preparations were being made, Joji slipped into the dome through a back entrance. He procured a plasma rifle and used stealth tactics to make his way deep into the heart of the facility. When the Markalite Cannons finally arrived on the battlefield, they began their offensive immediately. The rays seemed to work as the dome gradually weakened.

Meanwhile, the women aboard the Dome were freed by a dissenting Ryoichi, as Joji continued to delve deeper into the base. He fired at their machinery, which further weakened the defenses of the dome. Joji soon found himself in dire straits however, as he was nearly killed by the guards. Luckily, Ryoichi bailed him out just in time. The captured women and Joji escaped, leaving Ryoichi, who planned to sacrifice himself. He yelled one final message to his friends, warning that humankind should not become like the Mysterians and must halt the reckless use of atomic weaponry.

As the humans escaped the dome, the Mysterians warned the world to stop their assault, lest they retaliate with even greater force. The humans refused, so the Mysterians used their powers to send a flood barreling into one of the Markalite Cannons. The wall of water rushed across the countryside, and an entire village was completely obliterated. A second Moguera appeared underneath the other Markalite Cannon, prepared to wreck havoc. Luckily, it was crushed by the gargantuan weapon as it fell to the ground.

Inside the dome, Ryoichi continued to destroy more machinery as he noticed the scarred bodies of his enemies. The extra-terrestrial leaders evacuated as the BETA Class began to fire its electron gun. Before Ryoichi can reach them however, they were gone. Ryoichi walked off; he understood he would not make it. The dome erupted in a massive explosion. The BETA Class fired at a few of the escaping UFOs, but many still managed to get away. They docked with their Mothership and retreated into space, for their destiny was clear. The Mysterians would remain vagabonds of the universe, forever.