This episode focuses on the life of a refugee living in Japan. He has plans to "reset the world" and change things. But are his plans merely violent daydreams, or something more sinister?
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.
A routine live-fire exercise goes wrong, leaving a fleet of AI controlled helicopters flying above a refugee area, firing on anyone who comes near. And a mysterious and creepy man known as Gohda arrives to tell Section 9 how to handle it.
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.
Saito recounts his first run-in with the Major, and how he became part of the group that would eventually become Section 9.
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?
The Prime Minister is alerted to the existence of "hub cyberbrains," while Ishikawa returns from the peninsula to report on what he found out about Kuze's past.
The Major heads to Taiwan to investigate a lead on Kuze, and ends up getting involved with local gangs and a troublesome kid.
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.
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?