Clockwork Planet

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.

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.

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.

As soon as Naoto hears that RyuZU's sister is slumbering in the basement, he agrees to help with her rescue. After numerous trials, they finally make it to the lower floors of the Core Tower, but the countdown for the purge keeps ticking.

Though Marie and Naoto managed to foil the plan of the Kyoto Grid purge, they did not find RyuZU's sister AnchoR.

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.

In order to save the people from the giant weapon, Naoto and Marie become terrorists and take over the Akihabara Grid. In the now empty city, the army clashes with the giant weapon while RyuZU faces off with her weaponized sister AnchoR...

By registering Naoto as her master, AnchoR is finally free from her terrible fate. From the cube that she holds, Vermouth appears. He tells the group that the giant weapon Yatsukahagi is powered by electro-magnetic technology.

In order to fix RyuZU and Halter after the electromagnetic attack, Naoto and Marie head to the Ueno Grid to meet Konrad. There, Vermouth tells them the true aim of the Yatsukahagi!

In order to demagnetize the Akihabara Grid, Marie and Naoto decide to take over the Pillar of Heaven: the center of all the grids in Japan.

Along with Marie's old school friend, Houko Hoshinomiya, Naoto and the others observe the coup d'etat when they get a report that the Japanese government is going to use the Tall Wand against the Yatsukahagi.

While Naoto and Marie are attempting to reconstruct the world, AnchoR goes off on her own to stop the Yatsukahagi's rampage. Can the two geniuses stop Gennai from destroying the world that Y had created?!