Foreign embassy employees are held hostage and one killed by cyborgs geishas that have become evil. After a temporary standoff, Section 9 gets the situation under control and then sends Motoko and Togusa to determine why an undercover operative was present and targeted for death.
Section 9 must stop a state-of-the-art tank.
Section 9 begins to investigate the self-destruction of a line of Jeri Robots. They discover that the creator of the robots gave them each a virus that causes the destruction.
Togusa receives a call from an old friend.
The Laughing Man threatens to murder another person in Section 9, but Chief Aramaki thinks the Laughing Man has a more dubious plan.
The Superintendent General becomes the target of dozens of people infected with a virus by the Laughing Man. But when Togusa and Batou hunt down the supposedly infected killers, they find only a few were really infected.
Section 9 trails a South American revolutionary hero who has seemingly survived six assassinations.
Kusanagi investigates where organ donations are coming from after a girl mysteriously gets a heart transplant.
An investigation begins into the origins of a serial killer who leaves his victims to decompose. Togusa is told to watch an out-of-sorts Batou, whose strange behavior is in some way linked to the serial killer.
Togusa's memories are put in danger when she goes undercover at a mental institution for children suffering from Closed Cyberbrain Syndrome.
The robot that assist Section 9 wanders away from the compound and helps a young girl to find her dog. The robot also finds the cyberbrain of a dead filmmaker who traps people who log onto his program to force them into being his audience.
Section 9 investigates the sudden appearance of an heiress that has been missing for sixteen years, but who has aged seventy years in that time.
A group of people in a chat room talk about a recent assassination attempt by the mysterious Laughing Man. As the people try to determine theories as to the Laughing Man's identity, Kunasagi uses a fake identity to see if anyone in the chat room will admit to being the assassin.
Togusa investigates a cold case involving the kidnapping of the Serano Corporation's president by a person calling himself the Laughing Man. But during the process his friend, who had asked him to investigate, is murdered.
A tank prototype gets loose from a research academy and starts going on a rampage. Section 9 is brought in to investigate and stop the tank if necessary. When it starts heading towards Tokyo, the operatives realize they will have to destroy the tank.