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.

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.

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.