In the realm of Clockwork Planet, a mysterious clockwork master named Y reconstructs Earth using data and gears, reviving the once lifeless planet. Naota Miura, a high school student with extraordinary hearing, can discern the minutest gear rotations. His fascination with clockwork sets him apart from his peers. One fateful day, a container crashes into Naota's home while he showers, revealing a pristine automaton named RyuZU inside. As he endeavors to restore her, Naota unknowingly triggers a series of events that will alter the destiny of humanity.