At the Ministry of Science, fervent Professor Ochanomizu alongside his coworkers strive to reactivate Atom—the first robot with a human heart. Atom is the masterpiece of enigmatic Professor Umatarou Tenma, who built the android to replace his deceased son Tobio. However, while Tenma inexplicably shut down his brainchild and disappeared, Ochanomizu refuses to let such a major breakthrough in science go to waste.

Despite having the appearance of a nine-year-old, Atom not only possesses incredible strength and intelligence, but he is also endowed with a remarkable conscience and compassion that rivals humans. Sadly, the mechanical boy soon faces rejection and learns that not everyone is as welcoming as Ochanomizu. Although automatons have integrated into society, they are accepted only as tools and even seen as an upcoming threat to mankind's dominion.

Dreaming of a world where people and robots can prosper together, Atom dedicates his existence to protecting the lives of both and inspiring them to form genuine bonds.