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. Seeing the little girl reminds Motoko of her own past. When she 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.
Chat! Chat! Chat!
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 CIA arrives in Japan with a request to help them hunt down a serial killer. The killer, a former CIA operative, has recently gone rogue and has turned up in Japan. He is an especially brutal killer, preferring to skin his victims alive in the pattern of a T-shirt. This sparks an odd reaction in Batou, and his normally laid-back demeanor is replaced with one of furious determination. What is the link between Batou and this man?
Togusa goes undercover at a hospital for patients with Closed Cyberbrain Syndrome, a hospital completely cut off from communication with the outside world. Disguised as a staff worker, he learns that the patients' unique conditions make them exceptional at programming and hacking defense barrier programs.
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. After the adventure with Miki is over and the Tachikoma returns home, the members of Section 9 discover the box, and find that within it is a movie theater that contains the Ghosts of all those who saw the movie. Will Motoko be the next victim?
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! When a team of special operatives was sent in, all contact was lost. Section 9 is assigned to go in and determine what's really going on.
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". Worried, the Major calls Batou to a meeting; the Tachikomas, having suspicions of their own, attempt to eavesdrop on their conversation. What will be the fate of Section 9's Tachikomas?
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.
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 and Mr. Serano discuss what happened six years ago, and why Mr. Serano hasn't fulfilled his promise. This time, however, things are going to be different, with or without Serano's help.
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.
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. Batou goes to Motoko's apartment, even though he's sure its under surveillance. Once inside, he is attacked by the troops, but discovers Motoko's secret weapons cache and manages to fight back. But when the Armed Suit shows up, things start to go badly.
Stand Alone Complex
Togusa has been released from jail. But his badge and gun are confiscated, 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! It seems that Section 9 is still alive and well after all, but what about the Major?