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 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. Unfortunately, a female cyborg assassin named Fem has arrived first. Now it's a showdown between the Major and Fem, and a man's life hangs in the balance.
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.
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.
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.