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. [Written by MAL Rewrite]

Based on the comics by the late Nekojiru. Contains 23 animated shorts aired TV Asahi Network's show "Bokusho Mondai Boss Chara Ou." and 4 unbroadcast episodes.

August 1945. In a converted theological seminary on the outskirts of Nagasaki, a young doctor works to help his patients, as unsettling news comes of a new weapon used by the Americans on the city of Hiroshima. When the second nuclear weapon is dropped on Nagasaki, the hospital staff must work to save lives in the midst of the concentric circles of death that their city has become.

Chinami and her friends have formed an organization called OZ, with the financial backing of the Kujo Group. Their goal is to peacefully integrate people with Type-E abilities into society, and oppose the Foundation, an organization which seeks to capture and control Type-E users for their own mysterious purposes.