The United States, 2045. Working as mercenaries, the Major and her team, including newbie Stan, defend a gated town from outlaws. Togusa takes a call.
Armed by a generous patron, the Nomads attack Section 9 with AI drones. Togusa accepts a new mission from Japan's peace-seeking Prime Minister.
As Togusa dives into cyberspace to track his former team members, the group is detained by a mysterious American organization seeking to employ them.
While researching the team's disappearance and John Smith, Togusa takes a calculated risk. The GHOST members question the true nature of their mission.
Aramaki sets off after Kusanagi in a race against time. GHOST begin their assignment, but Huge's cybernetic security forces them to alter their plans.
Following the Section 9 reunion, Kusanagi and her colleagues learn about the "post-humans," a previously unknown threat to humanity.
Back in Japan after six years, Batou decides to take a break while waiting for his delayed team. Then some amateur bank robbers interrupt his fun.
The Major and Smith clash over Section 9's new mission hunting post-humans. She orders Togusa to investigate a suspected spy near the Prime Minister.
Problems arise for Section 9 after one of the three post-humans in Japan murders several politicians, then targets the Prime Minister's father-in-law.
Section 9 investigates a possible post-human hacker who uses the web to incite physical attacks on people. The trail leads to a high school student.
Pudding helps analyze the Thinkpol program while the Major and Togusa search for clues about the post-human middle school student Takashi Shimamura.
Togusa has a strange episode while analyzing the data confiscated from Shimamura. When he wakes up, he and Batou head out to investigate.