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.

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.

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.

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

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.