A series of android suicides prompts Section 9 to investigate the manufacturer, Genesis Androids. While Aramaki questions the plant manager, Kusanagi and a Tachikoma covertly hack into the plant's database to try to uncover any possible wrongdoings by the manufacturer. As it turns out, all the androids were of the same model, an obsolete product known as the GA07-JL android, dubbed the Jeri by its small but loyal fanbase. The Genesis Jeri-model android was popular because of the ease with which an end-user could modify it to their own specifications. While the plant manager half-jokingly comments that the Jeris have grown despondent because of their obsolete status, Kusanagi discovers that a virus has been inserted into the mainframe, probably by an end-user who had sent his Jeri back to Genesis for refurbishing, which infected other Jeris sent in for maintenance and compelled them to destroy themselves. Section 9 eventually discover that the culprit is Marshall McLachlan, the son of the Canadian ambassador to Japan. After the embassy revokes McLachlan's diplomatic immunity, the team confront and arrest him, and learn that he had fallen so much in love with his Jeri that he considered her an actual person instead of an android, and wanted to eliminate the other Jeris so that she would be unique.

Yamaguchi, an old friend of Togusa's and a police detective working in the Laughing Man task force, is murdered after he calls Togusa, requesting to see him concerning what Yamaguchi terms "suspicious internal activity" by superiors in the police department. At Yamaguchi's wake, Togusa is approached by Yamaguchi's wife, who delivers an envelope from him to Togusa that contain a series of strange photographs. Upon scrutinizing the photographs, Togusa realizes that none of them are taken using a camera. Continuing his investigation, Togusa interviews another detective in the Laughing Man task force, who coincidentally mentions that the task force is waiting to bug a primary suspect in the case with cybernetic surveillance devices called "interceptors". The interceptors allow constant audio and visual monitoring of the subject via their own senses. Togusa concludes that the Laughing Man task force members were bugged with these devices illegally for monitoring. Shortly thereafter, the information about the illegal use of the interceptors is leaked by Section 9, prompting the police Commissioner to call a press conference regarding the growing scandal. The Commissioner publicly denies any responsibility, instead blaming the head of the "Laughing Man" task force, Kunihiko Nibu, and announcing Nibu's immediate resignation. News reporters press the Commissioner about the possible involvement of higher officials, as well as the Commissioner's own ties to nanomachine maker Serano Genomics, Inc., who manufactured the interceptors, but the Commissioner continues in his denials. At that point, the hacker known as the Laughing Man returns. Hijacking a police official's cyberbrain, the Laughing Man denounces what he refers to as the "previous farce", and announces that due to the police's efforts to cover up the truth, he will reluctantly challenge them again. Finally, he delivers a death threat to the commissioner, stating that he will "remove" him if the truth is not revealed in full.

Kurutan calls the Major to the hospital where she works to look into the source of a young girl's heart transplant. The heart she received was given without consent of the owner's parents. The girl's doctors feared she might have had to be given a full-cyborg conversion, a thought that stirs painful memories for Kusanagi. Aramaki, believing that the culprits may be tied to a mass kidnapping ring, orders Section 9 to look into the case for connections between the organs, the company that sold them, and a local refugee camp set up at an abandoned oil refinery. Finally, the culprits are revealed to be a gang of rich medical students. Before arresting them, Kusanagi decides to scare and humiliate the students by posing as a murderous yakuza enforcer.

Marco Amoretti, 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. American CIA officers have been dispatched to Japan, ostensibly to assist Section 9 in their effort to track down and apprehend Amoretti before he can strike again. When the CIA officers show no surprise at the developments in the case, Ishikawa hacks into the CIA database and learns that Amoretti was part of an American Empire commando team sent into the jungles of South America to conduct a covert operation aimed at breaking an enemy’s will to fight by using terror tactics, such as flaying civilians alive. Elsewhere, Batou — an ex-JGSDF Ranger who has seen first-hand the horrors of the CIA operation — resolves to stop Amoretti by any means necessary, but his behaviour during the case leads to suspicion that Batou may attempt to kill Amoretti, rather than arrest him. However, this is exactly what the CIA wishes, since Amoretti is the only loose end that can tie them to the jungle operation. Amoretti's hideout in the sewers is discovered, and Batou gives chase in a running gun battle. Batou experiences vivid flashbacks during the chase, with the dank sewers intercutting with the steaming jungle where he first battled Amoretti years ago. Batou finally manages to corner Amoretti, who begs Batou to kill him. However, Batou remembers that he is a law enforcement officer first, and arrests Amoretti instead. The CIA agents, unhappy that things didn't go as planned, are forced to return home with Amoretti in tow.

Acting on a tip, Section 9 breaks up a cabal of thieves planning to rob a Japanese financial institution. Shortly after the raid, a Chinese intelligence official contacts Section 9 and informs them of suspicious activity that he believes may indicate an assassination attempt by Chinese Socialists on Kanemoto Yokose, a prominent, yet reclusive, Japanese billionaire. Section 9 is therefore tasked with protecting Yokose, a 56-year-old ex-mathematician who has amassed a fortune by playing the stock market. Section 9 and the assassin arrive within minutes of each other, but after reaching Yokose’s bedroom, both sides discover that Yokose died from a medical condition several months ago, and an advanced computer program had been managing his investments the whole time.

Following the nuclear World War III and the non-nuclear World War IV, Japan passed an act known as the Refugee Special Action Policy, inviting war refugees from all across Asia to enter Japan. Thousands of Asian refugees took Japan up on the offer to enter their country, and have taken low-paying jobs handed out to them by various companies looking for a cheap work force. Gino, a combat pilot and World War IV veteran, is one such refugee, working as a helicopter pilot for a corporate CEO. He is angry and depressed and plots revenge against Japanese society, starting with assassinating his employer. When Section 9 is sent to investigate his plots, Kusanagi eventually concludes that Gino lacks the fortitude to act out his fantasies, and is just one in the long line of pitiful souls who dream about fulfilling goals they can never accomplish.

A formal investigation into millionaire businessman Mr. Tadokoro has yielded evidence that he may be managing former Secretary General Yakushima's assets. This prompts the government to launch its own investigation into the allegations, but there are two problems. First, Tadokoro's vault is state of the art, and only he can access the assets in the vault. The other, more immediate concern is that a hacker and thief by the name of Cash Eye plans on infiltrating the vault during an exclusive high society party. To keep Cash Eye from stealing and/or destroying valuable evidence, Section 9 is called in to prevent the theft. However, the Cash Eye threat is revealed to be a ploy by Section 9 to find a cache of illegally laundered money, with Kusanagi posing as Cash Eye. They trick Tadokoro into opening his own vault, where they find the money.

The Tachikomas locate a stealth gate accessible only through the European satellite system; after passing through the gate, Borma recovers a suspicious file believed to be the virus that infected the Individual Eleven. Ishikawa and Borma attempt to figure out how the virus in the file affects its victims by using the external memories of an infected Individual Eleven member. They succeed in learning that the virus is activated by reading all of Patrick Sylvester's previous essays in addition to The Individual Eleven, but in making this discovery Borma is seemingly rendered comatose by the virus. Meanwhile, Togusa is sent to search for a written copy of "The Individual Eleven", the political essay bearing the same name as the terrorist group, but no matter where he looks, no one seems to be able produce an actual written copy of The Individual Eleven. When Togusa decides to make one last stop, he unexpectedly finds himself confronting a suicidal man who has become infected with the virus, and learns from him that there never was a written essay by that name. Elsewhere, Kusanagi, Batou and Saito have been dispatched to Kagoshima after the man behind the attempt on the prime minister's life unexpectedly turns up on an IR system near the city. The man, named Hideo Kuze, has gone there to rendezvous with the other leaders of the Individual Eleven. Section 9 intends to arrest Kuze at the Kagoshima war memorial, but Kuze and the other assembled members of the Individual Eleven leave before Section 9 arrives. As Kuze and the Individual Eleven drive to Kyūshū they share the stories of their crimes to pass the time, until they reach the Kyūshū Radio Tower. Upon reaching the roof of the tower, the group commits mass suicide by mutual decapitation with katana on live television. Kuze, however, fights off his partner and escapes.

A patient undergoing a routine medical procedure unexpectedly takes a turn for the worse, and the medical staff mount a frantic effort to save him. During the operation it becomes necessary for the doctor in charge of the operation to access the man's external memories, at which point he identifies his patient as the terrorist "Angel's Feathers", one of the world's most wanted men. After struggling over whether to protect doctor-patient confidentiality or inform the police of his discovery, the doctor finally opts to do the latter. The information he gives the police sparks a multi-national counterterrorism operation, with several nations sending members of their best special forces teams, including Batou and Kusanagi. During the briefing in Berlin, they learn that Angel's Feathers uses high-explosive bombs on glass-fronted high rise buildings to kill his targets, and acquired his nickname from the thousands of glass shards that rain down as a result of these explosions. The man in charge of the briefing explains that they have reason to believe Angel's Feathers will stop in Berlin before proceeding to his next target. While staked out on a cold night, Batou oversees a blind girl named Theresia searching for her father, who turns out to be Angel's Feathers; his regular trips to Berlin were to visit her. Batou and Kusanagi infiltrate the church that serves as their meeting place and are forced to apprehend Angel's Feathers in front of Theresia.