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.

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.

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.

It's spy vs. spy as D-Agency and Wind Agency both race to prevent Japan's "Grand Strategy" from falling into enemy hands.