Major Kusanagi and Section 9 are called in to resolve a hostage crisis at a Geisha house staffed by an android Geisha. Then Aramaki is approached by a friend who reveals that one of the hostages in the Geisha house was under investigation.
A heavy-assault multiped tank runs amok under the control of an unknown hijacker. After going on a destructive spree at the Kenbishi Industries testing facility, the multiped takes off towards the urban area of Niihama.
A series of android suicides prompts Section 9 to investigate the manufacturer. While Section Head Daisuke Aramaki questions the plant manager, Kusanagi and a Tachikoma covertly hack into the plant's database.
An old friend of Togusa's named Yamaguchi is murdered after sending him pictures concerning an unsolved case involving a hacker known as The Laughing Man.
Section 9 suspects that the police investigators handling The Laughing Man case are using their primary suspect, a former Serano Genomics, Inc. programmer with a shady anti-corporate past.
Things go fairly haywire as Kusanagi suspects that The Laughing Man has inserted a virus into the police units guarding the Superintendent General.
It has come to the attention of the Minister of Home Affairs that Jenoma revolutionary leader Marcelo Jarti has been visiting Japan regularly every five months.
Kurutan, a friend of Kusanagi's, calls the Major to the hospital where she works to look into the source of a young girl's heart transplant. It seems that the heart she received was given without consent of the owner's parents.
Kusanagi enters a chat room dedicated to The Laughing Man. Various crackpot (and a few plausible) theories are passed around JFK-style as the chat room members view various bits of evidence from the Laughing Man case.
Marco Amereti, a former American Imperial Navy Petty Officer turned serial killer, has arrived in Japan and for the last two months has murdered several women by slicing the skin off their torsos in the form of a t-shirt.
The Ministry of Health, Labor, and Welfare has been hacked into and classified material from their database has been stolen.
Early in the morning, Baton's Tachikoma self activates and leaves the Tachikoma storage bay to explore the outer world. While roaming the streets of the city the Tachikoma encounters a young girl searching for her lost dog.
Sixteen years ago Aka Turkuro, the daughter of a pioneering cyber company CEO, was kidnapped by a group opposed to cyberization.
Acting on a tip, Section 9 breaks up a cabal of thieves hell bent on wrecking a Japanese financial institution.
Kusanagi's reservations regarding Section 9's Tachikoma units comes to a head.
Sensitive information has been stolen from a U.S. Navy base and the primary suspect is a former Olympic silver medalist named Zaitsev.
Major Kusanagi and Chief Aramaki are visiting London for an anti-terrorism conference.
After a five-year wait, Chinese vice foreign minister Jin has been allowed access to the Kagashewa war memorial in Japan.
Former Japanese Prime Minister Kanzaki’s daughter has been abducted and Section 9 is called in to investigate her disappearance.
After the events of PORTRAITZ, Togusa uses J. D. Salinger's The Catcher in the Rye as a starting point and develops a theory that The Laughing Man is after something published on paper.
Togusa finds himself in the hospital after being shot, but is desperate to impart what he's learned to the rest of the group.
The Head of the DEA is arrested for murder in connection with the raid at the Sunflower Society building.
The Laughing Man returns to again kidnap the CEO of Serano Genomics, just as he did six years before.
Having learned the entire truth behind the Laughing Man incident from The Laughing Man himself, and having confirmed the information with Mr. Serano, Section 9 is finally ready to make their move against the man behind the corporate terrorism.
Aramaki has been released under his own recognizance and meets with the head of the Ministry of Justice to explain the situation and ask for help in ensuring his team members safety.
After 15 days of fierce fighting, the Umibozu complete their operation to dismantle Section 9 by assassinating Kusanagi and capturing Batou.