With Major Motoko Kusanagi missing, Section 9's Batou is assigned to investigate a string of gruesome murders—seemingly at the hands of faulty gynoids, or sex robots. But when a faulty gynoid leaves Batou a cryptic message, he begins to question the cause of their malfunctions. Suspicions of politically motivated murder and an illegal "ghost" quickly crop up, drawing Batou and his partner Togusa into a perilous web of conspiracy.

As their investigation goes on, the line between man and machine continues to blur, and reality and perception become indistinguishable. Confronting strange and dangerous foes, Batou and Togusa explore a futuristic world filled with machines and living dolls but utterly devoid of humanity.

[Written by MAL Rewrite]

The film is set in London at the end of the 19th century and after the attempted assassination of the Imperial princess in the television anime. The Empire is increasing counter-spy actions in the wake of the incident, and finds Control, the Commonwealth group in charge of covert operations against the Empire, at unease and suspecting its spy within the royal family as a double agent. Control assigns their spy ring Dove with a new mission to extract a secondhand bookstore owner and deliver him to Commonwealth hands. Ange, Dorothy, and Chise successfully spring the bookstore owner from an Imperial prison. Control also assigns Dove to make contact with Bishop, their spy within the royal family, to ascertain their loyalties. (Source: ANN)

In the town of Clock Hill, there is an old boarding house called Maison Ikkoku. While the residence itself is fairly normal, most of its occupants are not. Yuusaku Godai, its most quiet tenant, has finally reached his limit with his neighbors' constant disruptions and boisterous partying. Wanting a calmer place to call home so that he can study in peace, he prepares to move away. However, his plans to leave are suddenly interrupted when he meets the new boarding house manager, Kyoko Otonashi. Falling madly in love with her, he decides that the boarding house may not be such a bad place to live after all. Unfortunately for him, Kyoko has her own romantic troubles: she is a widow whose husband died six months into their marriage. And despite her blossoming feelings for Godai, Kyoko still cherishes her dearly departed husband, and she believes that no other man could possibly fill the void in her heart. But with Godai's persistence and some help of the other eccentric tenants, she may experience true love once again. [Written by MAL Rewrite]

In near-future Japan, Aya Okamura lives alone in an apartment away from her parents. Her mother has worked overseas ever since her childhood, so her aging father Kouji and their cat Mii-san are the only ones left in their family home. After a tiring day, Aya declines her father's invitation for dinner by lying that she is still at work. Yet that very night, she receives another call with sudden news that may bring this separated family closer. [Written by MAL Rewrite]