Clockwork Planet is an artificial celestial body created by the elusive and enigmatic clockwork master known as Y. He single-handedly rebuilt the Earth with nothing more than reams of data and gear parts, breathing life into a planet dead for a millennia.

Naoto Miura is a not-so-ordinary high school student who possesses exceptionally acute hearing. His gift allows him to hear the turning of even the smallest gears on the planet. He is obsessed with clockwork, so he spends his days toying with gears, making him an outcast at school.

One day, while Naoto is in the shower, a large container suddenly crashes into his apartment. Inside it, he discovers a beautifully preserved automaton by the name of RyuZU, and decides to repair her. Little does Naoto know that this encounter with RyuZU will turn the gears of fate, forever changing the course of humanity.