Three years following the resolution of the Babylon Project conspiracy, the members of Kiichi Gotou's Patlabor squad have dispersed. Gotou stays with the unit, joined by Shinobu Nagumo, his romantic interest and ally.
Capitalizing on the public's mistrust of Japan's Ground Self‑Defense Force, a clandestine terrorist group infiltrates the military to spark widespread destruction and civil chaos across the nation. Nagumo discovers that the mastermind behind this escalating plot is none other than Yukihito Tsuge, who has been manipulating events from shadows, 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.