The year is 2030. Six months passed since the Laughing Man Incident was solved. About 3 million refugees are living in Japan, invited to fill the labor shortage. However, the emergent presence of the invited-refugees intensified their confrontation with the "Individualists", who called for national isolation, which then led to the increased incidences of terrorist attacks. Under these circumstances, a terrorist group called the Individual Eleven carries out a suicide attack. But there was a greater scheme behind their action. When Section 9 learns this, they attempt to nail down the mastermind of the incident. Meanwhile, Kuze, a surviving member of the Individual Eleven, becomes a charismatic leader of the invited-refugees and intensifies the confrontation against the government. And Motoko starts feeling a strange sense of fate connecting her with Kuze...

故事发生在遥远的2061年，网络成为了维系社会平衡不可或缺的存在，并且已经发展到了凭借意识就能够自由连结的地步，然而，网络的极度发达带来的却是个人信息的不断泄露和被篡改，并且因此而引发了一系列严重的社会问题，犯罪事件频发。 为了保护个人隐私和安全，一个名为“Meta Real Network”的新型网络空间被发明了出来，在那里，名为“Bubble Shell”的防火墙保护着人类的记忆不受侵犯，然而，在这绝对安全的空间里，却有一批犯罪分子利用网络空间的漏洞进行着全新模式的犯罪，为了将这些罪犯捉拿归案，名为“电脑Diver”的探员们出动了，在解决事件的同时，探员们亦在慢慢靠近真相的核心。

As members of ESWAT, the elite forces serving Olympus, Deunan and Briaereos are deployed anywhere trouble strikes. Olympus finds itself under a stealth attack - cyborg terrorism, deadly nanotech zealots, and rioting citizens are just some of the threats that Deunan must contend with as she fights to save Olympus!

In a utopian society created at the end of the third world war, a female warrior who has been plucked from the badlands begins to see cracks in this new facade. And what does this community have planned for the rest of humankind?

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.