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.)

East Tokyo United (ETU) has been struggling in Japan's top soccer league for the past few years. It has taken everything they have just to avoid relegation. To make matters even worse, the team has lost five matches in a row, leading to abysmal team morale. Even the fans are beginning to abandon them, and rumors hint that the home ground municipality is going to withdraw their support. With countless coaches fired and poor financial choices in hiring players, it is a downward spiral for ETU. The board of directors, under pressure from general manager Kousei Gotou, takes a gamble and hires a new coach—the slightly eccentric Takeshi Tatsumi. Though considered a great soccer player when he was younger, Tatsumi abandoned ETU years ago. However, since then, he has proven himself successful as the manager of one of England's lower division amateur teams. Tatsumi's task won't be easy; ETU fans call him a traitor, and the team is pitted against others with larger budgets and better players. Yet even the underdog can take down a goliath, and Tatsumi claims he is an expert at giant killing.