The anime's story is set in 2027, one year after the end of the fourth non-nuclear war. New Port City is still reeling from the war's aftermath when it suffers a bombing caused by a self-propelled mine. Then, a military member implicated in arms-dealing bribes is gunned down. During the investigation, Public Security Section's Daisuke Aramaki encounters Motoko Kusanagi, the cyborg wizard-level hacker assigned to the military's 501st Secret Unit. Batou, a man with the eye that does not sleep, suspects that Kusanagi is the one behind the bombing. The Niihama Prefectural Police detective Togusa is pursuing his own dual cases of the shooting death and a prostitute's murder. Motoko herself is being watched by the 501st Secret Unit's head Kurutsu and cyborg agents. (Source: ANN)

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.

In the year of Tenpo 14, Yoi, monsters from another world attack Edo. Those who fight against them are members of Bansha Aratemesho. In public, Bansha Aratemsho is known as an organization to study foreign books. In fact, they are a organization dedicated to destroying the Yoi. These warriors are called Ayakashi. They gather information of odd events in the country, and are sent to destroy Yoi who appear. They are generally very strange people. For example, a guy who has lost his memory, a girl who dresses like a man. They have special powers with which to beat the Yoi. (Source: AniDB)

A.D. 2034. It has been two years since Motoko Kusanagi left Section 9. Togusa is now the new leader of the team, that has considerably increased its appointed personnel. The expanded new Section 9 confronts a rash of complicated incidents, and investigations reveal that an ultra-wizard hacker named the Puppeteer is behind the entire series of events. In the midst of all, Batou, who was stalking the case on a separate track, encounters Motoko. She goes away after saying, Stay away from the Solid State Society. Batou is left with a doubt in his mind. Could Motoko be the Puppeteer? The series of intriguing incidents that Section 9 faces gradually link together almost artistically. Who is the Puppeteer? What will happen to Batou's relationship with Motoko? What is the full truth behind this carefully planned perfect crime? And what will the outcome be? Mysteries surround the Solid State Society... (Source: Production I.G.)