Detectives Kusumi and Hata launch an investigation into the surge of labor accidents happening in Tokyo Bay. Their discoveries uncover a government cover-up related to a lethal biological weapon called WXIII-Wasted Thirteen, and a shocking personal connection for Hata. To stop the imminent danger, the detectives must work with the military, leading to a climactic showdown between the Special Vehicle Division 2's Labor force and WXIII. Taking place between Patlabor Movie 1 and 2, this film serves as a side story.