Tazuna is a high school student, living in Osaka, who loves to fiddle around with machines. One day, he receives a repair request from an university laboratory. He accepts the request and ends up meeting a girl named Koyori, who has been bedridden for a very long time. Suddenly, Tazuna and Koyori get pulled into a whole different world called “Ziggurat”. In this world, there are Hand Shakers, two people who touch hands and create the Nimrod. Their goal is to defeat other Hand Shakers in order to gain an audience with “God”, who will grant them wishes. Protect with your own Hands!

Taking place in the year 1937 on the eve of World War II, the story involves a mysterious spy training organization known as the "D Agency." The organization is established by Lieutenant Colonel Yuuki from the Imperial Japanese Army. His ideals lead him to recruit people beyond military academy graduates and personnel, while training them to become skilled agents in arts of manipulation. These agents would become a specialized team to conduct operations. One such antihero agent, under the name Jirou Gamou, goes on a harrowing mission to uncover secret documents titled "Black Notes," while battling forces from within and without his own ranks.

Bored with life, popular high schooler Yatora Yaguchi jumps into the beautiful yet unrelenting world of art after finding inspiration in a painting.