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.

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.

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.

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.

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.

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.

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.

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.

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.

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

=A hacker and thief by the name of Cash Eye plans on infiltrating a vault during a party, and Section 9 is called in to prevent it. But there are a number of strange elements in this case that don't all add up.

A seemingly run-of-the mill hit-and-run turns into anything but when Togusa investigates. While in Tokyo, he discovers a secret from the past the GSDF is trying to keep hidden deep underground.

During a scheduled maintenance, the Tachikomas begin to chat away about the Individual Eleven. While talking in their new "forum", Batou and Togusa appear and take one of the Tachikomas - who just happens to be Batou's pet - with them to Spring-8 to look at the scientific evidence gathered on the Individual Eleven.

Following a tip, the Major conducts an undercover investigation of Kuze in Taiwan. While there, she saves a boy running from the Mafia.

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.

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!

A group of terrorists identifying themselves as the "Individual Eleven" barricade themselves within the Chinese Embassy. Section 9 is called in to eliminate the terrorists without any civilian casualties, all before the scheduled police raid.

An assassination threat has been made against Prime Minister Kayabuki; Section 9 is called to serve as bodyguards Meanwhile, investigation on the Individual Eleven turns up some interesting history.

Plans have been leaked to terrorists that the plutonium recovered from the underground nuclear facility in Tokyo is to be moved. Section 9 is called in to ensure the plutonium reaches its destination, and Gohda is there again.

The Tachikomas and the Major continue to investigate Gohda and his motives, while the rest of Section 9 are out to stop a string of suicide bombings.

Togusa is brought up on charges after he becomes involved with a murder while off duty. But during the course of the trial, it becomes clear who the attorney is really after.