The story of The Empire of Corpses takes place in 19th century Europe, and revolves around John Watson. He is scouted by the government to become a secret agent- However, Watson lives in a world where “Frankensteins”- human corpses that are re-purposed with a false soul in order to use them as laborers- are used to improve industrial development.

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.

Blackouts and other mysteries at NAZKA Academy hint at an impending alien invasion.