Section 9's next case is a rash of mass-kidnappings. Rumor has it that a crime syndicate is harvesting organs and selling them on the black market. As they research the case, they realize that time is running out.

Section 9 is on the trail of Marcelo Jarti, a South American revolutionary hero who has arrived in Japan. However, Jarti is a hard man to catch because he employs look-alikes to deceive people. Nevertheless, Section 9 is convinced that the one they're tracking is the real thing, and after a rather out-of-control gunbattle in an upscale hotel, they track him to an old warehouse.

In a briefing, Aramaki shows a photo of a girl who looks like Eka Tokura, the daughter of Tokura Electronics, who was kidnapped 16 years ago. But there's one problem–the photo was taken two days ago!

Aramaki attends the funeral of an old war buddy, and is greeted by his departed friend's daughter. Later, Section 9 is assigned the task of protecting the Chinese Foreign Minister from being assassinated.

A certain type of android, the GA07_JL, nicknamed Jeri by its users, has been affected by a virus. Recently, all Jeri model androids have been committing "suicide". Section 9 is called in as it may be related to a virus detected in an android at the National Assembly Building.

Motoko enters into an online chat room devoted to the Laughing Man to see if she can find any new information on him. What she discovers is a spirited debate among the self-proclaimed "fans" of the Laughing Man, but very little hard evidence.

The Chinese government contacts Section 9 to let them know that an assassin may have entered Japan to kill a famous reclusive millionaire. Despite their considerable efforts, however, Section 9 is unable to contact him to warn him, so they go directly to his residence.

While at an international police conference in London, Aramaki drops by to visit an old flame who's now in the wine brokering business. She asks him to help her put a stop to the corruption in her company, but he tells her that it's out of his jurisdiction. Just then, however, two thieves break into the building and take them hostage.

The Laughing Man returns! And, just as he did six years ago, he kidnaps the president of Serano Genomics without being detected. Section 9 arrives at Serano's house too late, and sets out to find him.

The Laughing Man, having returned after a six-year absence, threatens to assassinate the Superintendent-General of the police. Aramaki, however, thinks it's a cover-up. He briefs Section 9 on the prime suspect, Nanao=A, an incredibly gifted programmer who developed the micro-machines that are currently the foundation of Serano Industries.

Motoko's friend Courtin asks her to come to the hospital where she works. It seems a little girl just received a heart transplant, but the donor's family doesn't remember ever agreeing to donate the heart. When Motoko mentions this story to Aramaki, he tells them to determine if this is tied to a ring of black-market organ smugglers supposedly run by the mafia.

One of the Tachikomas decides to take a little stroll through the city. It meets a little girl, Miki, who is searching for her lost dog and it agrees to help her. On their journey, the Tachikoma finds a strange box.

The Major has become worried about the Tachikomas. It appears that their AIs have developed much more quickly and in ways that were not anticipated; they have begun speaking about their "individuality".

Motoko is about to be fitted for her new prosthetic body. But when the doctor arrives and begins the procedure, it's clear that she has no intent of letting Motoko out alive. Meanwhile, Aramaki receives a disturbing message that his brother has been kidnapped.

Public Security Section 9 is an elite special ops unit that works directly under the control of the Prime Minister. They've been called in to rescue a high-ranking government official from a hostage situation. But something doesn't seem right to Major Motoko Kusanagi.

While working late, Togusa gets a call from one of his colleagues from his days on the police force. It seems that he's uncovered something strange happening with the investigators in the Laughing Man Unit, a special task force formed to catch the infamous cyber criminal known only as the Laughing Man. But before he can meet with Togusa, he's killed in a car accident.

Batou goes undercover on a military base to shadow one of his former heroes, a man named Zaitsev who was an Olympic silver medalist. Now, however, he's under suspicion of espionage. Batou befriends him easily, and the two really seem to get along--which is unusual for Batou. But when Batou learns the truth behind his hero, he must make a very difficult decision.

Togusa goes undercover at a hospital for patients with Closed Cyberbrain Syndrome, a hospital completely cut off from communication with the outside world.

Togusa has been released from jail and he's given papers showing the dissolution of Section 9. Out of work and depressed, he tries to find information on the others, but there is nothing available. Thinking that he has nothing left to lose, he goes to assassinate the man responsible when he is stopped by–Batou!

As Togusa and Bato track down Nanao, Motoko and Paz are attempting to protect the Superintendent-General at a press conference about the police misuse of interceptors. When the virus does hit, Motoko and Paz have to act fast to save the intended victim. Meanwhile, the road to Nanao=A hits a dead end.

While on a stakeout of a Taiwanese vegetarian restaurant, Section 9 finds out that someone is pulling strings and feeding misinformation to the Public Safety Sections.

With the latest Individual 11 incident still fresh in the public's mind, Section 9 discovers that only a skilled face sculptor could have created Kuze's prosthetic face. Since only two artists fit that description, they quickly locate the craftsmen and go to question them.

The Prime Minister is alerted to the existence of "hub cyberbrains," while Ishikawa returns from the peninsula to report on what he found out about Kuze's past.

Togusa is on the trail of the Laughing Man again, and this time, his investigations lead him towards both a leading micromachine corporation and an NGO called the Sunflower Society.

A refugee living in Japan has plans to "reset the world" and change things. But are his plans merely violent daydreams, or something more sinister?