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.

Members of Section 9 seek out a man named Philip Kukushkin, a Russian national who seems to know a lot about the creation of posthumans.

US special operations forces join the Section 9 team in their fight against a relentless posthuman named Suzuka Mizukane.

While extracting information from Kukushkin, the Section 9 team uncovers some shocking information about an AI program developed by the US government.

Worried Purin might be a spy for the Americans, the Major sends out a crew of Tachikoma to look into her hidden past.

Togusa finally realizes that he's been trapped in his own memories — and suddenly finds himself in a devastated Tokyo in the year 2045.

After hearing from Togusa, Batou and the others head to Tokyo. Back in Fukuoka, the Major learns that a posthuman has hijacked a nuclear submarine.

Resurrected as a full-body prosthetic cyborg, Purin tries to hitchhike her way to Tokyo. US special operations forces face Mizukane's wrath.

Batou and the group get an update on the posthuman situation from Standard. The Major and Purin join the rest of the crew in Tokyo.

To take back control of the hijacked nuclear submarine, the Section 9 team targets Mizukane and Takashi Shimamura.

Shimamura wakes up and makes a desperate move, putting Kusanagi and her crew in an impossible position.

Kusanagi and her team do everything they can to stop the US from implementing their draconian plan to end the nuclear standoff with "N."

The Section 9 crew start living their regular lives as if nothing ever happened — and the only one who finds it strange is Kusanagi.