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. [Written by MAL Rewrite]

The year is 2046. Detective Ross Sylibus is transferred to Mars when a country singer on her flight is murdered. Making matters more complicated is that the singer is a "Third"—a robot that looks and feels like a human. Sylibus is partnered with Armitage—a beautiful female cop with a bad attitude. As they investigate the murder of the singer and other women on Mars, they uncover a conspiracy that can have them both killed by the Martian government.

In the year 2046 humans are moving away from using robots and begin to trust them less and less. In this time life becomes very perilous for the beings known as seconds. The seconds are the most recent line of robots, as far as the public knows. This is the world Detective Ross Sylibus lives in. Detective Sylibus is transferred to Mars by his request after his partner was killed by a robot. As he arrives he falls headfirst into a murder where a country singer on his flight was murdered. He steps off the plane and watches as a scene unfolds and he meets his partner, Armitage a female cop with a major attitude. A rash of murders begins when yet more women are killed. As the investigation is continued a secret is uncovered. There is another line of robots known as Thirds. More and more Thirds turn up missing, as a serial killer who is intent on wiping out all the Thirds runs rampant. Armitage in her quest to put the murderer to justice reveals a secret. She herself is a Third.

A criminal group known as Demon Seed terrorizes Tokyo with its vast armies of mecha. The local police is afraid to confront them, but one person stands in their way: Maron Namikaze, a 13-year-old idol singer with a catchy voice and unbelievable superhuman strength.