The year is 2029. The world has become intensively information oriented and humans are well-connected to the network. Crime has developed into a sophisticated stage by hacking into the interactive network. To prevent this, Section 9 is formed. These are cyborgs with incredible strengths and abilities that can access any network on Earth. A mysterious new hacker known only as the Puppet Master threatens to create chaos, erasing and rewriting the memories of his victims: humans who have cast away their physical body to become cyborgs. Is he an evil genius, or could he signal the beginning of a new age in the relationship between man and machine?

The year is 2032. Following the events of the first Ghost in the Shell movie, Major Motoko Kusanagi has since left her physical body and is now a "ghost" living in the network. This leaves Batou as the top officer at Section 9, the special task force assigned to matters of human/machine relations. Batou's latest assignment is to investigate the recent string of suicide-murders perpetrated by a certain brand of "gynoids," androids designed to look like women. Together with officer Togusa (one of the last few people who hasn't had his body fitted with cybernetic parts), Batou tracks down the cause of the wayward gynoids — all the while pondering and discussing the hazy realms where machines become dangerously close to human, and humans become dangerously close to machines.

Alerted to a possible conspiracy active amongst the highest levels of the Police, the members of Section 9 discover that a previously inactive but elite hacker may be involved in the blackmailing of several key business and government leaders. As the conspiracy stretches to affect all levels of society, time is running out for Major Motoko Kusanagi and her team to uncover the truth and capture the elusive Laughing Man. Released in the United States and Canada on October 2, 2007, this film is an OVA version of the first season of the anime series Ghost in the Shell: S.A.C.

Unlike The Laughing Man, which stuck to the storyline of the TV series, Individual Eleven has gone through a bold editing phase, and the relationship between Kuze and Motoko is even more highlighted than in the TV series. This is a re-born 2nd Gig. 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.

In 2029, with the advance of Cyborg technology, the human body can be "augmented" or even completely replaced with cybernetic parts. Another significant achievement is the World of Ghost in the Shell#Cyberbrains, a mechanical casing for the human brain that allows access to the Internet and other networks. An often-mentioned term is "ghost", referring to the consciousness inhabiting the body (the "shell").

Uchikomatic Days is a 5-minute short telling the story of the birth of the Uchikomas, the 'ugly duckling' second generation think-tanks that made substandard replacement models for the Tachikomas. The short features a music performance by the A.I. Tough Guy Uchikomas, a group of rising stars that will provide entertainment at the Harima City for Academic Research New Year's Eve Party.