In the ambitious Babylon Project, Tokyo undergoes a major urban transformation with the aid of Labors—specialized robots used for construction. These machines are essential to the rapid development of artificial islands in Tokyo Bay. When the key figure behind this project is found dead under suspicious circumstances that appear to be suicide, Captain Kiichi Gotou and his Patlabor team are assigned to uncover the truth. Meanwhile, a series of Labor malfunctions and a corrupted AI system endanger the lives of Tokyo's residents. Young pilot Noa Izumi, together with her Patlabor named Alphonse, works under Gotou's leadership to stop a potentially apocalyptic scheme aimed at destroying both the city and the country.

In this installment

Three years after the Babylon Project scandal concluded, the members of Kiichi Gotou's Patlabor unit have gone their separate ways. Gotou continues serving with the Patlabor team, alongside Shinobu Nagumo, who is both his colleague and romantic interest. A terrorist group, exploiting the public's distrust of the Japanese Ground Self-Defense Force, emerges from within the military and launches a series of attacks that plunge Japan into widespread chaos and civil unrest. Nagumo discovers that the mastermind behind these acts is Yukihito Tsuge, her former mentor and ex-lover. Gotou reassembles his original Patlabor team, led by pilot Noa Izumi, to apprehend Tsuge. As they pursue their mission, Nagumo must confront her complicated past ties to help restore peace to Japan.