Devastated over losing his only child in a car accident, Dr. Umatarou Tenma, the director of the Ministry of Science, mobilizes the institution's entire staff to create Atom: an ultimate technology robot made in his late son Tobio's exact image. Aside from unmatched power and intelligence, the robot also possesses the innocence and playfulness of a young boy.

However, Atom fails to meet Tenma's expectations when the latter realizes that Tobio's replacement cannot grow. Unable to recognize Atom for what he is, Tenma wishes to forget the whole affair. Dismissing the feelings of what he considers just a machine, he cruelly sells the android to a robot circus that treats its performers as merely disposable tools. Despite his predicament, Atom shows kindness to his wretched kin and humans alike, sparing no effort in times of crisis to keep everyone safe.

Soon, fortune smiles on the mechanical boy, as Dr. Ochanomizu—a visionary who fights against the abuse of robots—frees him from the circus. Under Ochanomizu's guidance and with a chance to forge a path in their mixed human-robot society, Atom fights tirelessly to make the world a peaceful place while also discovering its vast complexity.