The masterminds behind the Health and Labor Ministry's scandal that Section 9 was after are arrested. Togusa could do nothing but watch the news. He was hoping to be reunited with his comrades who had gone missing since the incident began. Meanwhile, alone in the National Library Museum, where all of the print media are collected and stored forever, the man who is thought to be the Laughing Man awaits a reunion with someone.

One by one, the members of Section 9 are hunted down and captured. Batou stops by at Motoko Kusanagi's safe house and confronts two arm suits ambush. Barely defeating the enemy, he manages to escape and joins up with Kusanagi, but...

Aramaki attempts to trap the mastermind of the Laughing Man case. But unidentified arm suits enter Section 9 facilities to take control. Kusanagi abandons the facilities and orders all members to get away and go into hiding. But the hunters were already reaching their hideouts.

A hooded figure is standing in front of the house of Serano Genomics CEO Ernest Serano. The Police Agency is interested since this reminds them of the modus operandi used by the kidnappers six years previously in the early years of the Laughing Man Case. And Section 9 is ordered to take care of the case.

Aramaki's brother was discovered in a refugee ghetto, and Aramaki, on his own, heads for the hospital where his brother is hospitalized. Kusanagi, on the other hand, goes out to get her cyborg body remounted after a confrontation with Gail. They were both not aware that there were remnants of the drug intervention enforcement squad in town.

Aramaki's brother was discovered in a refugee ghetto, and Aramaki, on his own, heads for the hospital where his brother is hospitalized. Kusanagi, on the other hand, goes out to get her cyborg body remounted after a confrontation with Gail. They were both not aware that there were remnants of the drug intervention enforcement squad in town.

Speculating from an oil painting scribble at the vocational training institution, Togusa comes up with what seemed to be the truth of the Laughing Man Case, and he volunteers to investigate files at the Health and Labor Ministry. He comes across an NGO named Himawari Group, which aims to spread an unauthorized drug for cyber-sclerosis. Just as he was visiting the group, he gets involved in an incident.

Former Prime Minister Kanzaki's daughter Reiko suddenly disappears. Is this a disappearance or a kidnapping? A personal grudge or an act committed by organized crime? Section 9 is frustrated by information restrictions, leaks and confused information. Eventually, a female spy, who was involved in numerous organized crime incidents, emerges in the investigation.

Aramaki receives a request for help from the daughter of an old colleague. At first he rejects the request, since he could not let personal matters get in his way. In the meantime, he intercepts some highly confidential information; someone is plotting to assassinate the Chinese Vice Foreign Minister. It became apparent that the earlier request and the plot were related. Aramaki moves to prevent the assassination, but...

Aramaki and Kusanagi were visiting the UK to attend an international conference on terrorism. Afterwards, Aramaki heads to a bank where an old acquaintance works, and gets involved in a startling incident. Kusanagi tries to rescue Aramaki from outside. Could they predict each other's plans and actions to free Aramaki?

Batou was sent to the military as an undercover agent to find a spy who was leaking top secret information. He encounters a hitherto undefeated wrestler who was famous for his unique timing and skill of "catching cyborgs off guard". This was until he finally lost a match. Seeing his hero silver medalist in disgrace, Batou explodes with his fists.

A Chinese assassin named Fem comes to Japan. She has a grudge against Yokose, a well-known billionaire. To achieve her mission, the fascinating killer acquires a deadly weapon, and heads for Yokose's mansion. Section 9 is dispatched to prevent the murder. Kusanagi and Fem run into each other. What did Kusanagi see after the skirmish? "There is a ghost in this country that wanders about. It's a ghost called capitalism."

Kidnapped Eka was lost for more than ten years when she was found unchanged on an offshore plant. The coast guard requests Section 9 to investigate the site. Although the plant was located within the boundaries of Japan, outlaws controlled it. Non-cyber and non-cyborg guerrillas give them a hard time. Who is Eka anyway?

Two short stories comprise this omnibus episode. The Tachikoma, who restore memories from bits that remain in the body, goes into town and meet a girl who is looking for a missing dog. The Tachikoma brings back something incredible from a junkyard, which stirs up something within Section 9. How do the Tachikoma define life? And what did the Tachikoma pick up?

An extensive cyber attack on the Ministry of Health and Labor by a hacker leads to the leak of top secret information. The hacker is traced to a vocational training institute for cyber deficient children. Togusa conducts a covert investigation on his own and comes across an astonishing truth.

A cruel and strange series of murders has been taking place; its extreme nature and peculiar modus operandi reminding Batou of a mission carried out long ago. Batou tracks down the murderer in order to settle something from the past. What does Batou intend to do?

Back on the Net, the reappearance of the Laughing Man was the talk of the day. A dedicated chat room offers a wide range of ideas to help solve the case, and Kusanagi joins in to get to the bottom of it. She then notices someone monitoring the chat room. What caused Kusanagi's uneasiness for such a long time?

The Tachikomas, noticing a slight change in Kusanagi's manners, conclude that they will be disposed of by Section 9. They have a deep discussion over topics such as life, ghosts, AIs and their own raison d'etre. After long arguing, they come up with one decisive strategy, and eventually decide to step into action...

A heart transplant was carried out without the donor's consent. When Section 9 is called in to investigate, they come across a group that deals in illicit sales of organs. A victim who lost his heart and the heartless culprits... As one whose entire body was transformed into a cyborg while she was young, Kusanagi seems to have especially strong feelings about this incident. What has she got against these criminals?

A source had reported that a South American drug lord, Marcelo, was visiting Japan often. Section 9 was dispatched for an investigation. Marcelo makes contact with Japanese organized crime. What are his intentions? Eventually, local police forces join them in the effort to crackdown on organized crime. Now Four different factions jostle for control. And Kusanagi finally discovers Marcelo's secret, however...

It's the day of the forewarned assassination of the Police Commissioner. In the heavily guarded area, a sleeper virus sent by Nanao activates. Kusanagi, on patrol with Paz, Saito and Tachikoma, manages to stop the nightmare, but, soon after, a series of insurgencies spring up that have nothing to do with the virus. Sporadic they seem to be, but what could have triggered them?

Aramaki suspects the Laughing Man Case to be a police hoax. In order to get evidence to back his theory, Section 9 carefully examines Nanao, who is the prime suspect of the Special Investigative Division. At the same time, Kusanagi independently reviews another Laughing Man Case that occurred 6 years earlier. She seems to be onto something, and asks Aramaki if she could guard the Police Commissioner.

One rainy evening, Togusa gets a phone call from Yamaguchi, an ex-colleague from the ministry, who detected some suspicious moves within the police department, and wanted to consult him about it. Togusa starts up an investigation using photos forwarded by Yamaguchi. When Togusa finally solves the mystery, he sets out on a hunt to reveal the illegal use of a device within the Police Department.

A bizarre incident occurs: a mass suicide of androids. After an investigation, it turned out to be a deliberate crime using a certain virus. In the android factory, a strange protection code was found in the computer terminal. The suspect runs away, and Section 9 goes after the suspect. And what did they see? Do robots have souls?

A prototype intelligent tank built by Kenbishi Heavy Industries suddenly activates. The military, which was not entirely decided about approving the purchase, is unwilling to intervene in the incident and Section 9 is called in for assistance. Section 9 sends Tachikomas to hunt down the vehicle and he plans to fire on it where there are no residential buildings. But despite his efforts, the tank keeps rolling. It looks as though it's headed towards a specific destination. Where is it going? And for what reason?

The Foreign Minister and his delegation are kidnapped by android geishas. Motoko Kusanagi and the members of Section 9 rush to the scene and rescue the diplomats. After a continuous investigation, section chief Aramaki discovers that there was a conspiracy surrounding an important military secret file called the Ichinose Report. Could they keep the file from leaving the country?