At the top of a large structure in Tokyo Bay, a scientist walks to the edge and, despite the cries of onlookers, throws himself into the sea to his death. Weeks later, the Special Vehicle Division (SVD) has had little respite due to a recent rash of Labor malfunctions resulting in massive citywide destruction.

No one seems to know the cause of the malfunctions; the only hint points to a cover-up involving a military-class Labor going on a rampage — without a pilot. It is soon evident that a disaster of epic proportions is taking shape, and only Gotou, Shinobu, and the SVD can counter it. If they succeed, they will be heroes... but if they fail, they will be the most hated villains in history.

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Sequel: Kidou Keisatsu Patlabor 2 the Movie
Alternative setting: WXIII: Patlabor the Movie 3
Parent story: Patlabor: Mobile Police