Following the Babylon Project conspiracy resolution, Kiichi Gotou's Patlabor unit split up, except for Gotou and Shinobu Nagumo, who stayed together due to their camaraderie and romantic feelings. As the public grew more skeptical of the Japanese Ground Self-Defense Force, a terrorist group infiltrated the military to cause chaos and civil unrest. Nagumo learned that her former lover and mentor, Yukihito Tsuge, was behind the dark scheme. Gotou gathered his former Patlabor team, including pilot Noa Izumi, and urged them to thwart Tsuge. Nagumo had to face her complicated past relationships to save Japan.