The year is 2045, and artificial intelligence has undergone tremendous developments. Governments use them as weapons, engaging in never-ending warfare to sustain their economies. The mercenary group GHOST, headed by Major Motoko Kusanagi, is no stranger to this landscape. However, the rapid innovation of this technology causes a new threat to loom over the horizon. Having left Public Security Section 9, Kusanagi and her group are involved in many operations worldwide related to these proxy wars. But a seemingly simple job of locating an arms dealer drags GHOST into a hidden conflict against cybernetically enhanced individuals, who have inexplicably gained extreme intelligence and physical abilities. Dubbed post-humans, their emergence sets off a chain of events leading to the reunion of Section 9. Armed with a new mission, it is up to Kusanagi and her reestablished team to prevent global chaos at the hands of these post-humans.

One day, manga author Shin Karino is greeted by four-year-old Kotarou Satou, his new next-door neighbor, who gifts him a box of tissues. In Karino's eyes, Kotarou is an odd kid: he speaks in an extremely formal manner, and he lives alone in his apartment—no parents or relatives in sight. But Kotarou neither seems to mind, nor wants to rely on people. Feeling sympathetic toward Kotarou's circumstances, Karino decides to follow Kotarou to a bathhouse in case something might happen to him and there he comes to understand the little boy is not so different from him. Little by little, Karino—along with the other residents of the apartment complex—grows fond of Kotarou and his antics. At the same time, Kotarou himself might have found something akin to a family in his unique neighbors.

The path to becoming a fine wife begins with being an accomplished cook—at least, that is what Ryou Machiko's late grandmother had led her to believe. For a middle schooler, Ryou's cooking skills are incomparable; but recently, though Ryou's food looks appetizing and smells inviting, the taste has not been delicious. Just when the dejected art student comes to terms with the possibility that she might continue living alone for the rest of her life, her aunt tells her that Kirin Morino—Ryou's second cousin—will begin staying with her every weekend since the younger girl has joined a cram school in Tokyo and aims to attend the same school as Ryou. Surprisingly, with her cousin's arrival, Ryou finds that her cooking has vastly improved—apparently, it is not her prowess in the kitchen, but the sharing of the experience with those closest to her that seems to make the flavors shine.

Compilation film of Koukaku Kidoutai: SAC_2045 with new scenes.