Autumn, 1937. Against the Imperial Army's objections, Lt. Colonel Yuuki establishes the spy training group "D-Agency." The army sends Lieutenant Sakuma to serve as their liason to D-Agency, and he watches the applicants easily coast through the brutal examination process. Not long after, Sakuma is ordered by Colonel Mutou to search the home of a suspected American spy, the Japanophile John Gordon. Disguised as military police, Sakuma leads D-Agency on their first mission.

Aaron Price, Far East correspondent for the British Times, investigates the true identity of Lieutenant colonel Yuuki, the man rumored to have founded D-Agency. Flipping through the Military Preparatory School's list of past enrollees, his eye is drawn to a boy who passed the entrance exam at the top of his class, but was expelled for violence. His name? Akira Arisaki.

Karl Schneider, writer for the Berlin Allgemeine, is suspected of being a German/Soviet double agent. While D-Agency searches for proof of his espionage activities, Schneider suddenly dies under mysterious circumstances. Lieutenant Colonel Yuuki sends his men on individual missions in order to uncover the truth.