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.
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. Now, Togusa only has an envelope full of seemingly random photos to go on--can he put the pieces of the puzzle together?
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?
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.