Three years after the Babylon Project conspiracy is resolved, the members of Kiichi Gotou's Patlabor unit have gone their separate ways. Gotou remains with the Patlabor team, accompanied by Shinobu Nagumo, his romantic crush and comrade. Playing into the public's skepticism toward the Japanese Ground Self-Defense Force, a terrorist organization begins to work from within the military to cause destruction and mass civil unrest throughout Japan. Nagumo learns that the mastermind behind the growing terrorist plot is none other than Yukihito Tsuge, her former mentor and lover. Gotou reassembles his former Patlabor team, spearheaded by pilot Noa Izumi. Leading the team into a mission to arrest Tsuge, Nagumo must come to terms with her complicated past relationships in order to save Japan. The date is 2002, three years after the events of Mobile Police Patlabor: The Movie. The destruction of a United Nations Labor team in south-east Asia begins the build-up to a deadly terrorist plan that threatens to send shock waves throughout Japan's military.With evidence of an impending military takeover, the scattered members of the original SVD (Special Vehicle Division) must gather to defend the city against danger. To make matters worse, the mastermind behind the operation is none other than Nagumo's former teacher and ex-lover Tsuge. Can Nagumo stay true to her oath to uphold the law in the face of Tsuge's destructive plan for revenge?The countdown to armed revolution and panic on the streets of Tokyo begins now...