A piece of Kyoto, one day that 1000 years had passed since the earth was destroyed and played back as a clockwork planet. Suddenly a black box fell down under Miura Nao, who lives surrounded by watch and gear with machine geeks -! It appeared from inside, crown of a beautiful girl's automatic doll (Automata). I tried repairing her by failing and not having to move, "sound" ....

Marie who encountered a crown that should have broke down moves. Knowing that the crown was repaired is Naoto and offer cooperation to avoid purging in Kyoto. And while heading for the core tower, Mary noticed the existence of a masterpiece trying to kill herself ....

I heard that crown sister sleeping in the basement and decided to cooperate Nao. I finally infiltrated the deep part of the core tower and I worked hard, but the purge time was approaching moment by moment. Meanwhile, Naoto will be forced to make a big decision that may lose the crown -!

Successfully planned · Stop the purge of Kyoto Naoto and Mary, but there was no crown sister, Uncle. Short wave communication using illegal electromagnetic technology arrives under Mary who returned to daily life. A new conspiracy was hidden in the content that provoked Mary.

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...

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 freed from a continued fate as "The one who annihilates". From the cube that she holds, Vermouth, who sent the shortwave to Marie, appears. He tells the group that the giant weapon Yatsukahagi is powered by electro-magnetic technology. And in Akihabara, that same electro-magnetic technology stops all the gears of the city from turning.

In order to fix RyuZU and Halter who were rendered immobile due to the electromagnetic attack, Naoto and Marie head to the Ueno Grid to meet Konrad. There, Vermouth tells them the true aim of the Yatsukahagi. Will they be able to repair RyuZu and Halter in the limited time they have until the Yatsukahagi starts moving again?!

In order to demagnetize the Akihabara Grid, Marie and Naoto decide to take over the Pillar of Heaven, which is the center of all the grids in Japan. With the help of a weapon housing Halter's mind, they overrun the Sakuradamon Grid and take Souko Hoshinomiya hostage. They then make a big announcement, but what's the aim behind that?

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. As the time draws close to the impact of the Tall Wand, Gennai, the mastermind behind the coup d'etat, fires the Yatsukahagi's main cannon. The two geniuses, Marie and Naoto, face a new challenge in order to stop Gennai's rampage.

While Naoto and Marie are attempting to reconstruct the world, AnchoR goes off on her own to stop the Yatsukahagi's rampage. RyuZU, Halter, Vermouth are all fighting their own battles while hoping that the two could make a miracle happen. Can the two geniuses stop Gennai from destroying the world that Y had created?!