The story takes place in a trading city Ert'Aria. Leicester Maycraft is an item engineer belonging to an adventurer guild Oasis. One night, he is at a party with his friends to see a meteor stream on the rooftop of a chapel. One meteor grazes them and hits the steeple of the chapel. There he finds a secret room and a sleeping girl. The girl wakes up and says You must be my father! The encounter with the mysterious girl brings an unexpected adventure to Leicester.

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.

Japan in the near future suffers an unexplained major disaster. Five years later, reconstruction is well underway. Two young researchers at a university are pinning all their hopes on robot development. Now their new interpretation of the eternal hero Astro Boy up until his birth is just about to start! (Source: Showgate)

One day, when Remu Mikage is on a video call with his sister, Shiki, who has traveled to the futuristic Okinotori-island Mega Float City for school, she confesses that both the audio and visuals of her are completely artificial. In order to be more efficient in her studies, Shiki has used neural-linked nanomachines to upload her consciousness onto a computer and is storing her physical body in a body pool. While shocked, Remu is supportive of his sister's decision, until the disaster known as the Early Rapture happens. The Early Rapture causes everyone who has uploaded their consciousnesses to either fall into a coma or perish. Remu visits his sister's empty apartment one last time, but is shocked when Shiki arrives at the door. With no memory of her family or past, and being pursued by a violent group of researchers, Shiki and her brother are forced to flee using her newfound power of nanomachine manipulation.