A group of terrorists identifying themselves as the "Individual Eleven" barricade themselves within the Chinese Embassy. Section 9 is called in to eliminate the terrorists without any civilian casualties, all before the scheduled police raid.
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.
Batou and the Major are sent to Berlin in an international effort to help track down the terrorist Angel's Wing.
While tensions rise in the Dejima refugee camp, the Major hacks the refugee cyberbrain hub to determine Kuze's location.
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?