- The final episode completes the first stand alone series. Togusa is released from prison but has no idea what has happened to section 9 members and still can not believe that the chief abandoned them. Episode reveals what happened to the members of section 9 and has a long conversation with the laughing man that wraps up the series.—Dirk Jungquist
- Kusanagi and Aoi have a disembodied conversation, the Major has become a floating individual Internet entity when her remote cyberbrain was hit by the sniper's bullet. Aoi thanks her for keeping her promise.
Togusa sits sadly in casual clothes. He narrates the events of the last few weeks. Bitter at Aramaki, Togusa was arrested and held for 15 days, then released but with no job to go to. He tried to find out what happened while locked up, goes to the office ruins and a 'Net cafe and reads the news archives. The media reported the use of deadly force by the JSDF to foil the Section 9 plot for a coup. He learns that the Major was killed and the remaining members of Section 9 were serving time in prison. There was no mention of Aramaki at all. After three months of doing nothing Togusa decides on some action.
The TV news reports on Yakashima being investigated following the elections. Togusa realizes the news background info on the Micro Machine scandal came from Section 9. He believes Yakushima will get away with it so he takes his own gun and goes to the Ruling Party HQ. He is stopped by none other than Batou, who brings Togusa to Section 9s temporary HQ.
The rest of the team joke and laugh as they watch the Yakushima news and review the past. Batou explains that Aramaki planned the whole Section 9 sacrifice with the Prime Minister. Togusa is upset at not being in the loop but the others point out he was protected and safe as he was an "ordinary" man. Batou says they are once again an offensive organization that doesn't officially exist.
Aramaki and the Minister of Justice meet. The Minister offers Aramaki a role in Justice but Aramaki want to rebuild Section 9.
At the National Book Museum Kusanagi meets the young man Aoi, the fomer Laughing Man. The labyrinthine library had been his hideout the whole time. They discuss philosophy and his original motivation. He had accidentally found out about the Murai Vaccine/Micro Machine issue while diving in the 'Net. Aoi cites the phenomena of copies where no originals exist, Kusanagi terms it "Stand Alone Complex", where everyone is synchronized. Aramaki arrives to join the conversation, he offers Aoi a job with Section 9 to use his super hacking skills. The young man politely refuses saying he is not a team player and wishing to remain in an unused library to sort through and read it's collection of books.
Mr. Serano is escorted by guards in parking garage as he gets ready to be witness in court. An unknown man passes in the other direction. Serano goes to his car, lifts the door handle and stops wide-eyed at what he sees and hears (a beeping bomb). The passerby man talks to himself about adapting to survive.
The whole Section 9 team goes into action with an "A2 Loadout". Kusanagi jumps from the top of a high building.
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