The Babylon Project is a massive renovation of Tokyo's neighborhoods, including the creation of artificial islands in the Bay. Utilizing "Labors," or robots created for the express purpose of doing work, architects and construction crews are able to more efficiently progress development of the overhaul. When a key figure in the Project's conception is found dead after committing suicide under mysterious circumstances, Captain Kiichi Gotou's Patlabor police unit is tasked with getting to the bottom of the bizarre situation. As several Labors begin to go haywire and a hacked AI program endangers the people of Tokyo, young pilot Noa Izumi and her Patlabor Alphonse work under Gotou's orders to save the city and the entire nation from a massive biblical conspiracy. [Written by MAL Rewrite]

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]

This special follows the story of how Isaki Shuuji and Ruo Minai became Contracted Priest and Shikabane Hime.

Twenty-six-year-old Hiroto Suwa; his wife, Naho; and their old high school classmates—Takako Chino, Azusa Murasaka, and Saku Hagita—visit Mt. Koubou to view the cherry blossoms together. While watching the setting sun, they reminisce about Kakeru Naruse, their friend who died 10 years ago. Mourning for him, they decide to visit Kakeru's old home, where they learn the secret of his death from his grandmother. Filled with regret, Suwa and his friends decide to write letters to their 16-year-old past selves to set their hearts at rest. With the knowledge contained in the letter from his future self, 16-year-old Suwa has the chance to rewrite the future. What choices will he make? What will happen in this new future? [Written by MAL Rewrite]