It's been 1000 years since Earth has died and been reborn as the Clockwork Planet. One day, in Kyoto, a black box nearly crushes Naoto Miura, a nerd who surrounds himself with clocks and gears. Inside that box is a beautiful automaton called RyuZU. Since she is not moving, Naoto sets out to repair her, relying only on "sound".

The Meisterguild sent genius clocksmith Marie Bell Breguet to investigate the anomaly at the Kyoto Core Tower, while there, however, she notices that the army seems to be up to something. Meanwhile, RyuZU arrives at Naoto's school as a transfer student. The entire school is up in arms because the loser Naoto is with a girl as beautiful as RyuZU...

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. On their way to the Core Tower, Marie finds out who is behind all the attacks on her.

As soon as Naoto hears that RyuZU's sister is slumbering in the basement, he agrees to help. 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. Under pressure, Naoto is forced to make a decision that could end up in him 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. Behind the inflammatory content aimed at Marie, there is yet another layer of intrigue...

Marie and Naoto find AnchoR on the lowest level of the Mie Grid. However, she looks quite different than expected. During their fight with the weaponized AnchoR, Naoto and RyuZU fall into the deep underground. To make matters even worse for the devastated Marie, the existence of a gigantic weapon is unveiled...