Un grupo que se hace llamar Los once individuales toma rehenes en la Embajada China pidiendo un cambio de la política de refugiados asiáticos. Si la Sección 9 consigue resolver el caso sin problemas, será restaurada.

Un piloto oficial, ciborg veterano de guerra, del presidente de una compañía tiene sueños violentos de matarlo. ¿Realidad o fantasía?.

Un hombre de negocios informa a Aramaki de que un ladrón le ha informado que cometerá un robo en una fiesta organizada por él. La Sección 9 se infiltra para detenerlo en la extraña fiesta.

Después de la muerte de un piloto de helicóptero, su IA se vuelve hostil mientras otros comienza a comportarse de la misma manera. La Sección 9 de Seguridad Pública es requerida para resolver la situación.

Durante una visita a un campo de reufugiados, la Primer Ministro Kayabuki recibe una amenaza de muerte. El equipo de la Sección 9 debe por un lado protegerla y por otro descubrir el autor de la nota.

Aramaki empieza a sospechar cuando se descubre sin vida el cuerpo de un hombre que dice poseer información sobre una tapadera del Departamento de Energía. ¿Accidente o conspiración? Togusa se encarga de investigar la parte de Tokyo en ruinas después de la bomba.

La Sección 9 es encargada de transportar plutonio a un sector de refugiados. Días antes de la operación, un cargamento de armas desaparece en una operación reclamada por los Once Individuales y el equipo se prepara para una posible emboscada.

La Sección 9 sigue investigando a los 11 Individuales. La Mayor, Ishikawa, y Boma intentan conseguir información de un agente gubernamental, Ghoda, mientras que el resto intenta detener a uno de los 11 Individuales.

Aprovechándose de la situaión de los refugiados, unos terroristas cibernéticos lanzan unas bombas contra hombres de negocio, Batou y Togusa deben investigarlo. Mientras tanto, Motoko quiere infiltrarse en el sistema de Gohda para descubrir más sobre los 11 Individuales.

Togusa tiene un encuentro con un ciborg que persigue a una chica que finalmente es asesinada por él. Durante el juicio, la defensa del ciborg examina con lupa a Togusa mientras intenta probar que la muerte resultante fue un accidente.

Mientras se prueba a los nuevos candidatos a la Sección 9, Motoko se introducida en una tienda de recuerdos en un callejón surrealista y allí rememora los eventos traumáticos de su distante infancia.

Mientras se investiga el caso de los 11 Individuales, cámaras infrarrojo registran la imagen del intento de asesinato de la Primer Ministro Kayabuki. Mientras, Boma, Ishikawa y Togusa revisan los documentos de los 11 Individuales, el resto del quipo intenta capturar al cyborg.

El equipo de Daisuke Aramaki consigue seguir el rastro de un miembro de los 11 Individuales hasta un fabricante de caras de ciborgs asesinado antes de poder interrogarle. La grabación de la escena muestra como culpable a Pazu.

While on an assignment guarding the Prime Minister, Saitou and the Tachikomas pass the time playing poker with a few policemen who are also assigned to the case. Much to the chagrin of the other men, Saitou wins hand after hand.

The Tachikomas take notice of Saitou's uncanny accuracy and start to comment. Their constant chattering quickly gets on the other player's nerves, so to smooth things over Saitou recounts his time working as a sniper for mercenaries in Mexico.

During a scheduled maintenance, the Tachikomas begin to chat away about the Individual Eleven.

While talking in their new "forum", Batou and Togusa appear and take one of the Tachikomas - who just happens to be Batou's pet - with them to Spring-8 to look at the scientific evidence gathered on the Individual Eleven.

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

After being saved, the boy follows her, making sure that she finishes what she started. The mafia will continue to pursue the boy and the Major has to protect him.

The Major and Batou are flown to Berlin in an effort to track down a terrorist called "Angel's Feathers". While there, Batou attracts the attention of a young girl in a wheelchair.

The girl is waiting for the yearly visit from her father, but Batou's appearance piqued her curiosity. As the days lead up to her father's visit, her curiosity in this stranger grows stronger.

Despite close scrutiny by the authorities, the Dejima refugees declare their independence. Kuze is suspected to be the mastermind behind this new resistance and Section 9 is sent to detain him.

The Major hacks into the refugee cyberbrain hub and easily locates Kuze. When the team rushes to capture him, however, they find themselves in the middle of a trap.

Section 9 heads to Etorofu in search of Kuze. During their investigations, the Major finds an interesting floppy disk on the body of a dead addict.

The floppy proves to be a goldmine of information, as it contains records of plutonium transactions. The last buyer to purchase the material was a group of Asian refugees. Realizing the transaction is about to take place, the team rushes to the location and is surprised by what they find.

Much to the chagrin of Batou, Motoko, and the rest of the team, Kuze and the refugees manage to escape in one of the camouflaged boats. They are further hampered when an explosion causes heavy losses, leaving them unable to follow the fleeing boat.

Regrouping, the team decides to refocus the investigation to the events surrounding Kuze. They start a secret investigation into Sagawa Electronics, the company responsible for the nuclear material transaction, and find that Gouda was involved. Meanwhile, as the boat heads for Dejima, Kuze makes his own unsettling discovery.

The city of Fukuoka is evacuated when a live nuclear bomb is found. With the Dejima Refugees targeted as the prime suspects, the government sends the Self-Defense Forces into the city.

Aramaki suspects the CIS's involvement in this latest incident is deeper then it appears. Batou is sent to gather more information from Gouda, but will he be able to hold his temper against the arrogant agent?

The Chief Cabinet Secretary uses the excuse of the refugees possessing 10kg of plutonium to mobilize the military against Dejima. With the available evidence against the refugees, Prime Minister Kayabuki reluctantly agrees. However, she soon learns from the Chief Cabinet Secretary that he's aligned himself with Imperial America and is now after her job.

Knowing her days as P.M. are numbered, she agrees with Aramaki's plan and calls the U.N. in for a nuclear inspection of Dejima. The move buys them some time to defuse the situation, and Section 9 heads to Dejima to meet up with the U.N in two days. However, with tensions running high it is only a matter of time before someone fires the first shot.

With the felling of Dejima Bridge by the refugees, a rumor circulates around the Cabinet that the refugees plan a mass suicide bombing using nuclear bombs. Fearing this, the Cabinet steps up the attack against the city. Meanwhile, Prime Minister Kayabuki has been secretly arrested and taken to an unknown location. Aramaki, Togusa and Proto, in trying to help the P.M. are also taken into custody and secured in her office.

With Section 9 having entered the non-communication zone and Aramaki being cut off from communication, Ishikawa and a Tachikoma make their way to Spring-8 on their own. Meanwhile, Gouda has sent an unwitting Section 4 after Section 9 to retrieve the plutonium.

As the attack on Dejima escalates, the Major catches up with Kuze. She explains the whole situation to him and he agrees to follow her. They are about to leave when both are attacked by the Self-Defense forces and in the confusion are trapped under the rubble.

Togusa rescues the Prime Minister and brings her back to her office. There, Aramaki hopes her influence will stop the launching of the ultimate weapon. Meanwhile, Batou reasons with Section 4.

Kuze and the Major come up with a plan to save the refugees, but the chances of its success are slim. Realizing this, the Tachikomas disobey the Major's orders and come up with a plan of their own. Batou has also disobeyed the Major's orders to go to the bridge and is desperately searching for her in the ruins of Dejima. Meanwhile, the Prime Minister is frustrated with being spurned by the Chief Cabinet Secretary. Determined to be remembered as more than a mere figurehead, she takes matters into her own hands.