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.

A man wakes up with complete amnesia. His only posession? A passport with the name "Ryosuke Shimano" and the port of entry, Marseille. Speaking with to Alan, the mysterious man next to him, he learns France has been occupied by the German army.

Former diplomat Kiichiro Shirahata is suspected to have illegally gained knowledge of the Imperial Army's top-secret "Grand Strategy." Investigating in secret, Jirou Gamou makes contact with Shirahata's old friend, the British consul Ernest Graham.

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.