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.

A future where the continuity of history has broken off, a world of enormous ruins that continues endlessly. Oceans and continents have vanished, existing only within the archives brought up from the remains. Ura works in the Archive Excavation Department, which restores and analyzes the data left behind. One day, he finds a disturbing visual record... (Source: ANN)

Special Vehicles Division 2 is back on duty, along with their Ingram Patrol Labor (Patlabor) robots. Using their courage as well as the Ingrams, Captain Goto's motley crew of officers battle crime in Tokyo city. They also deal with their personal lives, as well as the supernatural. (Source: ANN)

In the far future, the elevated irradiation from the sun has destroyed the environment of the earth and the birthrate of humans has drastically decreased. The government controls society with an army of cloned soldiers called Ideal Children (IC). Sam Coyne is a trader in a desert. One day, he saves a beautiful woman Maya, who has been chased by Theseus, a corps of IC. He shelters her in his trade ship, but the destroyers of Theseus surround Sam and Maya.