In 2030 AD, even if the intention to run around as light and electrons is concentrated in one direction as the computerization becomes generalized and the information network becomes more sophisticated, by the time the "lonely person" becomes an "individual" as a complex. Is an era when it is not computerized. It depicts the activities of the "Public Security Section 9" (commonly known as "Ghost in the Shell"), which was established as an independent counterintelligence unit under the direct control of the Ministry of Home Affairs to counter complicated crimes. There are a wide variety of top-secret missions such as cybercrime investigation, terrorism deterrence / arrest, VIP protection, and corruption detection, but one incident emerges as it is carried out.

Set in 2032 AD. The truth is revealed through the appearance of the Cabinet Intelligence and Research Office, which is hostile to Section 9 from the background of the resurrection of Public Security Section 9, starting with the case of a terrorist who claims to be "11 individual people", and the appearance of the individual 11-person case and Kuze. Becomes. The information manipulation and crafting activities of the Cabinet Intelligence and Research Office will increase the distrust and opposition of the refugees, and the consolation refugees will be armed and uprising all at once.