Despite their best efforts, the remaining members of Section 9 are rounded up one by one by the government forces; only Batou and Motoko are left.

After being shot, Togusa's in the hospital and about to go into surgery, but he is desperate to pass on what he's learned to the rest of Section 9. As Togusa fights for his life, the rest of Section 9 takes over the case, but others within the government have learned of the investigation and are not happy.

The government orders Section 9 disbanded. Aramaki is taken away, and Togusa is arrested. Motoko assembles the remaining team members at HQ for one final mission. They prepare for a full-scale assault while Elite troopers and Armed Suits descend on Section 9 HQ.

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!

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.

Marco Amoretti, a former Navy Petty Officer from the American Empire, has come to Japan and is committing heinous acts of brutality against women. Section 9 is assisted in this matter by the American Empire's CIA. While this doesn't sit well with Public Security's members, Batou finds the whole case particularly hard on his psyche as the nightmares from his past rear their ugly head.

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.

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.

The tables seem to be turning in favor of Section 9, but the nuclear missile is still being prepared for launch.

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.

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

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.

Kuze manages to take down the jamming plane, but becomes trapped in rubble with the Major. The Tachikomas begin discussing what to do about the nuclear submarine they have spotted, and Batou manages to convince the special forces that have been sent to kill them to listen to him.

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.

While field testing new recruits, the Major finds herself hacked, and an old woman tells her a story from her past.

Kenbishi Heavy Industries has built a state-of-the-art multiped tank. There's only one problem–it's gone haywire and started moving on its own. Section 9 is called in to stop it, as the Self Defense Force will not get involved. Now, it's up to Motoko, Batou, and the rest of Section 9 to stop the tank and figure out what made it go berserk in the first place.

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".

The Prime Minister is taken into custody, and the military begins its strike on Dejima. The Major and part of Section 9 head to Dejima to try to hand over the nuclear device to the military there, in order to defuse the situation, while Ishikawa heads to SPring-8 to deliver the rest of the plutonium.

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!

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.

The Major and Batou are flown to Berlin in an effort to track down a terrorist called "Angel's Feathers". While there, Batou attracts the attention of a young girl in a wheelchair.