It's been 1000 years since Earth has died and been reborn as the Clockwork Planet; in Kyoto, a black box nearly crushes Naoto Miura; inside that box is a beautiful automaton called RyuZU; since she is not moving, Naoto sets out to repair her.

The Meisterguild sent clocksmith, Marie Bell Breguet, to investigate the anomaly at the Kyoto Core Tower; she notices that the army seems to be up to something; RyuZU arrives at Naoto's school as a transfer student.

Marie has a chance encounter with RyuZU, who she thought was broken all this time. When she finds out that it was Naoto who repaired her, Marie asks for his help to prevent the purge of the Kyoto Grid.

After numerous trials, they finally make it to the lower floors of the Core Tower and continue their work, but the countdown for the purge keeps ticking; Naoto is forced to make a decision that could end up in losing RyuZU.

While Marie and Naoto managed to foil the plan of the Kyoto Grid purge, they did not find RyuZU's sister AnchoR; Marie was going about her day when an illegal shortwave radio transmission reaches her.

Marie and Naoto find AnchoR on the lowest level of the Mie Grid; during their fight with the weaponized AnchoR, Naoto and RyuZU fall into the deep underground; the existence of a giant weapon is unveiled.