Legend tells that when the Earth was destroyed, the great clockmaker Y made a replacement from cogs and gears. Naoto Miura is a young boy who aspires to be a great clockmaker. However, despite his unique talent—sensitive hearing that can immediately understand clockwork mechanics from noise alone—he has made little progress. But this changes when a coffin falls from the sky into his apartment, revealing RyuZU, a female automaton forged by Y himself.

News of RyuZU's arrival brings Marie Bell Breguet, the gifted heir of a distinguished line of clockmakers, and her cyborg bodyguard Vainney Halter into Naoto's life as well. When she and Naoto both become embroiled in an action-packed battle for their lives, they discover an uncomfortable truth: the clockwork planet that humanity has lived on for over a millennium is beginning to break down—a secret that many people will kill to protect.