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.

Set along a backdrop of a fictitious second world war at an international city in Asia. In Japan, Lieutenant Colonel Yuki (Yusuke Iseya) recommends the creation of spy training school "D Kikan". Meanwhile, Kato (Kazuya Kamenashi) is facing capital punishment for his refusal to follow a superior's order. Kato is then scouted by "D Kikan". He goes through a harsh training regiment and faces his first mission as a spy. In order to seize American ambassador Graham's confidential documents "Black Note." Kato infiltrates into an international city. A battle to gain possession of the "Black Note" ensues between Kato, a mysterious woman named Rin (Kyoko Fukada), the British Spy Agency, the Soviet Spy Agency and the radical army in Japan.