After the resolution of the Babylon Project conspiracy, Kiichi Gotou's Patlabor unit disperses. However, Gotou and his colleague Shinobu Nagumo stay on board. As public doubt towards the Japanese Ground Self-Defense Force rises, a terrorist group emerges within the military, triggering chaos across Japan. Nagumo discovers that the orchestrator behind this upheaval is Yukihito Tsuge, her former mentor and romantic partner. To counter this threat, Gotou rallies his old Patlabor crew, led by pilot Noa Izumi, for a mission to apprehend Tsuge. Nagumo must confront her complex past entanglements to safeguard her nation.