While field testing new recruits, the Major finds herself hacked, and an old woman tells her a story from her past.
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While working late, Togusa gets a call from one of his colleagues from his days on the police force. It seems that he's uncovered something strange happening with the investigators in the Laughing Man Unit, a special task force formed to catch the infamous cyber criminal known only as the Laughing Man. But before he can meet with Togusa, he's killed in a car accident. Now, Togusa only has an envelope full of seemingly random photos to go on--can he put the pieces of the puzzle together?
Motoko enters into an online chat room devoted to the Laughing Man to see if she can find any new information on him. What she discovers is a spirited debate among the self-proclaimed "fans" of the Laughing Man, but very little hard evidence.
The CIA arrives in Japan with a request to help them hunt down a serial killer. The killer, a former CIA operative, has recently gone rogue and has turned up in Japan. He is an especially brutal killer, preferring to skin his victims alive in the pattern of a T-shirt. This sparks an odd reaction in Batou, and his normally laid-back demeanor is replaced with one of furious determination. What is the link between Batou and this man?
Togusa goes undercover at a hospital for patients with Closed Cyberbrain Syndrome, a hospital completely cut off from communication with the outside world. Disguised as a staff worker, he learns that the patients' unique conditions make them exceptional at programming and hacking defense barrier programs.
One of the Tachikomas decides to take a little stroll through the city. It meets a little girl, Miki, who is searching for her lost dog and it agrees to help her. On their journey, the Tachikoma finds a strange box. After the adventure with Miki is over and the Tachikoma returns home, the members of Section 9 discover the box, and find that within it is a movie theater that contains the Ghosts of all those who saw the movie. Will Motoko be the next victim?
In a briefing, Aramaki shows a photo of a girl who looks like Eka Tokura, the daughter of Tokura Electronics, who was kidnapped 16 years ago. But there's one problem--the photo was taken two days ago! When a team of special operatives was sent in, all contact was lost. Section 9 is assigned to go in and determine what's really going on.
After being ambushed by Kuze's followers at a false location, Section 9 is alerted to his true location, and his intentions of purchasing nuclear materials from the Russian mafia.The Cabinet Intelligence Service and Gohda are involved behind the scenes.
The entire city of Nagasaki is evacuated and the JSDF moves in after a live nuclear bomb is found planted in the city, presumably by Dejima militants. Section 9 arrives to defuse the bomb and determine its precise origins.
The Prime Minister is taken into custody, and the military begins its strike on Dejima. The Major and part of Section 9 head to Dejima to try to hand over the nuclear device to the military there, in order to defuse the situation, while Ishikawa heads to SPring-8 to deliver the rest of the plutonium.
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