为了打击“后人类”——一种突然出现在网络社会的新型人类——所犯下的网络犯罪，首相秘密下令重组公安九课。户草在搜寻可能已觉醒的岛村隆时失踪，为查明户草下落，草薙素子率公安九课前往已成为废墟的东京。在那里，草薙素子一行人遇到了自称“N”的难民组织以及一支美国特种部队。由于一艘被扣押的核潜艇引发了核战争的威胁，公安九课、美国和后人类之间的三方混战愈演愈烈。

笑脸男事件结束后，公安9课新的敌人是自称“个人的11人”的反政府武装组织。在其计划周密的犯罪背后，牵扯的战争难民问题更令整个社会的矛盾激化。面对政府与犯罪分子带来的压力，草薙素子再次带领公安9课出动。

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.