Set in the year 2000 (between the events of Patlabor and Patlabor 2), when the level of Labor accidents begin to escalate around Tokyo Bay, police detectives Kusumi and Hata are assigned to investigate. What they discover leads to a series of government cover-ups, conspiracy concerning a new biological weapon entitled WXIII-Wasted Thirteen and a tragic, personal connection to Hata. The only hope to stop this threat is to cooperate with the military and lead WXIII into a showdown with the Labors of Special Vehicle Division 2.

A mysterious suicide and a series of unmanned robot run-aways sparks off a Police investigation into the suspicious software on-board thousands of industrial robots around Tokyo.