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.
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.
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.
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.
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. With a corrupt police official on the outside, it's up to Aramaki to keep them alive and buy enough time for the Major to figure out what's going on.
Aramaki attends the funeral of an old war buddy, and is greeted by his departed friend's daughter. She tells him that her brother is acting very strangely, and she fears that he may be up to something illegal. Aramaki sympathizes, but says there's nothing he can do legally. Later, Section 9 is assigned the task of protecting the Chinese Foreign Minister from being assassinated. And when they start searching for suspects, the son of Aramaki's friend is at the top of the list!
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. If they don't find the kidnapped girls soon, it will be too late. And to make matters worse, there's a Russian cyborg operative who has gone rogue and is now working for the syndicate.
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. As he visits with one of the officers of the Sunflower Society, however, the building is attacked by especially well-armed troops!
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. A special forces unit is dispatched to intercept them with a state-of-the-art Armed Suit.
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. With Motoko's friend Courtin waiting outside and unaware of what's going on, Motoko must fight for her life. Meanwhile, Aramaki receives a disturbing message that his brother has been kidnapped.