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.

The raid of Gordon's home comes up empty. And when Gordon lets it slip that this is the second time his home's been searched, Sakuma realizes the mission is a set-up by Mutou.

Sergeant Eiji Honma has been assigned to the Shanghai military police. Not long after assuming his new post, he is summoned by Captain Masayuki Oikawa. Oikawa orders Honma to conduct an internal investigation and uncover an enemy agent who's infiltrated their ranks. As he explains the mission, they hear an explosion...

Kazuo Izawa has a good life running a simple photography store in London... until he's suddenly arrested under suspicion of espionage. As Isawa undergoes a harsh interrogation, Lieutenant colonel Howard Marks, master spy for the British Secret Intelligence Service, appears before him.

D-Agency receives an urgent meeting request from one of their collaborators, Morozoff, who has important secret information to report. D-Agency member Reiji Seto arranges to meet him on the South Manchurian Railway Asia Super Express. As Seto moves to collect the information, he finds Morozoff has been murdered.

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.