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.

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.