Section 9 tries to protect the richest man in the world from assassination, only to find out the man's computer has been impersonating the already dead man for months.
When the Als start to speak about their individuality, the Major starts to worry and has his team investigate.
Batou goes under cover to shadow one of his former heroes.
Chief Aramaki must figure out a way to escape when he and an old girlfriend are kidnapped while he is in Great Britain.
Section 9 is called in to stop an assassination of the Chinese Foreign Minister.
Section 9 is sent to discover what group is responsible for a recent rash of kidnappings and murders.
Togusa searches for the Laughing Man, who may know of a cure for the cyberbrain sclerosis that is starting to spread.
The Narcotics Department of Section 9 is sent to kill a cyberbrain sceloris sufferer who refused to approve drugs for sale to help others but took to save himself.
Secretary General Yakushima sends his Narcotics Department troops to frame and then murder Chief Aramaki and Kusanagi. But they manage to escape with help from Batou and the Laughing Man.
Under the pretext of being under house arrest, the head of the Serano Corporation is being protected by Secretary General Yakushima. Section 9 tries to get to him and bring him into custody before the Laughing Man attacks him.
After trying to protect Yakushima, the government decides that Section 9 has started to become too powerful and wish to disband it. Section 9 is attacked and when Borma, Togusa, and Paz are captured, the remaining fake suicide to escape custody.
The government starts rounding up all the Section 9 agents one by one. Batou does his best not to get captured, but an assault on him in Motoko's apartment turns deadly.
Togusa is released from prison and begins to search for other members of Section 9. He finds nobody until Batou stops him from making a mistake by assassinating the person who had put Togusa in prison.
Batou must go undercover to find out if his hero Pavlo Zaitsov is trading top secret information.
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