Since time immemorial, a cosmic entity known as Algol has watched over humanity. To determine whether Earth's people are worthy of venturing into space, Algol selects three individuals and awakens their latent potential, transforming them into superhumans called Elites. The three chosen are a weak-willed Japanese middle school student named Takiryu Taro, an American infant named John Kowalski who already possesses extraordinary psychic abilities such as telepathy, precognition, and teleportation, and a ruthless international criminal, Elkenig Dangar.

Dangar immediately seizes his newfound power to pursue world domination. He recognizes the baby John as the key to unlimited strength, because John alone among the three Elites has psychic gifts. Dangar murders John's parents and attempts to kidnap the infant. The third Elite, Taro, stands against him. Taro is an ordinary boy who wanted to be a manga artist, but now he must use his enhanced intellect and physical abilities to oppose Dangar. He develops a powered battle suit that grants super strength, flight via gravity control, and bulletproof defense, and he constructs a massive computer in the basement of his ally Dr. Solomon's mansion.

Dangar, who has already amassed a criminal organization and later uses brainwashing to swell his ranks, unleashes terrible weapons. He deploys a rifle that fires miniature atomic bombs called Pencil Baryon shells, devastating parts of Tokyo and earning him the epithet "Atomic Bomb Man." The United Nations declares him the number one enemy of humanity. Taro is aided by Judy Solomon, the daughter of a scientist who studies psychic phenomena, and by a police inspector who becomes a trusted ally. However, Taro's parents are kidnapped by the CIA, drugged and subjected to brainwashing, leaving them as hollow shells. The CIA agent responsible later regrets his actions and aids Taro.

Dangar, having turned his own body into a cyborg, returns to Japan for a final confrontation. Meanwhile, John Kowalski is protected by Taro and Judy. John's powers grow under the tutelage of a yogi and psychic master brought from India. The narrative unfolds as a struggle between the three Elites: Dangar's ambition for planetary and later cosmic rule, Taro's reluctant but determined heroism, and John's role as a being of pure potential. The story touches on themes of humanity's capacity for self-destruction and redemption, with the opening scenes referencing the Vietnam War as a backdrop. The question of whether humanity will annihilate itself or prove worthy of the stars rests in the hands of the Elites.