After an embarrassing high school class reunion with their successful classmates, who have proper jobs, relationships, and even children, the Matsuno sextuplets return home to sulk about their status as NEETs. They spend the night drinking away their sorrows, eventually falling unconscious, until they awaken in a strange world of memories, centered around one of the brothers' biggest high school regret. As the sextuplets navigate this memory world, they encounter their embarrassing past selves from high school, as well as those of their friends. All the while, they try to uncover whose regret was great enough to trap them in this strange world, so that they can make their way back to reality. However, they're running out of time; this world of memories is unstable, and the sextuplets may lose their chance to make things right if they're too slow....

Three hundred years ago, a genetic experiment gone wrong caused the mutation of all forests on Earth. Armed with consciousness, the vegetation sought to destroy all of humankind, and the war that ensued turned the planet into a hellish dystopia. In the present day, Agito, a young boy, lives with his father in Neutral City—a village maintaining an uneasy truce with the neighboring forest. One day, Agito, on his way to collect water, becomes separated from his friend and stumbles upon a relic of the past: a girl sleeping in a mysterious machine. Agito awakens the girl, Toola Cm Sacl, and introduces her to the village. But outside forces have ulterior motives for the girl, who holds the key to restore the Earth. Misguided by Shunack, a soldier from the old world hellbent on destroying the forest, Toola follows him despite Agito's warning. Determined to save Toola and unify humankind with the forest, Agito borrows the power of the forest and pursues her.

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.

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.