In 2000, a series of unknown attacks on Labors have made two police detectives, Shinichiro Hata and Takeshi Kusumi, investigate these string of events alongside members of the Tokyo Metropolitan Police Department's SV2 unit in solving the case in which the labors that were attacked belong to Schaft Industries.

As they begin to unravel the reason behind the attacks, the two detectives find out that the attacks may have something to do with the American military stationed in Japan, as well as elements of the Japanese Ground Self-Defense Forces, coupled with a female scientist involved in a biological weapons program known as Wasted XIII.

Two police detectives and SV2 investigate a series of mysterious acts of deadly destruction occuring in and around Tokyo Bay.

When several deadly Labor accidents suddenly strike Tokyo Bay, veteran police detective, Kusumi, and his young partner, Hata, take on the case. Each detective applies his own style of investigation, but neither is prepared for the international labyrinth of deceit that is about to unfold.

Hata's new girlfriend, a genetic research scientist, hides a secret that the detectives need and Kusumi vows to unravel. Soon, the investigators are entangled in a world of government coverups, military conspiracy, and personal tragedy. As the investigation heightens, the detectives encounter an unexpected enemy-- the ravenous biological weapon WXIII: Wasted Thirteen.

To stop the beast's rampage, Kusumi and Hata must work with the military to lure the monster into a brutal showdown with the Patlabors of Special Vehicle Unit 2!