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.

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.

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...

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.

The luxury liner Tokimaru makes its way from San Francisco to Japan, stopping at each Hawaiian island along the way. As Osamu Utsumi sits on the deck enjoying a crossword puzzle, he's approached by a man calling himself Jeffrey Morgan. At that same moment, cries of terror erupt from those looking out at the ocean.

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.

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.

Hermann Wolff, a Wehrmacht Colonel assigned to German's intelligence agency, the Abwehr, investigates a suspicious train crash on the outskirts of Berlin with his right-hand man, Lieutenant Johann Bauer. Among the belongings of one of the bystanders is one of a spy's standard tools of the trade. When interrogated, its owner claims to have stolen it from a Japanese man named "Katsuhiko Maki..."

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.