Motoko enters into an online chat room devoted to the Laughing Man to see if she can find any new information on him. What she discovers is a spirited debate among the self-proclaimed "fans" of the Laughing Man, but very little hard evidence.

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.

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.

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.

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.

Plans have been leaked to terrorists that the plutonium recovered from the underground nuclear facility in Tokyo is to be moved. Section 9 is called in to ensure the plutonium reaches its destination, and Gohda is there again.

The Tachikomas and the Major continue to investigate Gohda and his motives, while the rest of Section 9 are out to stop a string of suicide bombings.

Saito recounts his first run-in with the Major, and how he became part of the group that would eventually become Section 9.

Following a tip, the Major conducts an undercover investigation of Kuze in Taiwan. While there, she saves a boy running from the Mafia.

The government declares martial Law in Dejima, believing that the refugees have a nuclear device and plan to use it to gain independence. When the refugees' connection to Kuze is cut off, one shot begins a bloody war.