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.
While on a stakeout of a Taiwanese vegetarian restaurant, Section 9 finds out that someone is pulling strings and feeding misinformation to the Public Safety Sections.
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.
While field testing new recruits, the Major finds herself hacked, and an old woman tells her a story from her past.
Watch more Ghost in the Shell on [adult swim].
The Major heads to Taiwan to investigate a lead on Kuze, and ends up getting involved with local gangs and a troublesome kid.
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.
After being ambushed by Kuze's followers at a false location, Section 9 is alerted to his true location, and his intentions of purchasing nuclear materials from the Russian mafia.The Cabinet Intelligence Service and Gohda are involved behind the scenes.
Kuze escapes and Section 9 suffers heavy damages from the confrontation; Kuze leaves for Nagasaki harbor with the Russian package.
The entire city of Nagasaki is evacuated and the JSDF moves in after a live nuclear bomb is found planted in the city, presumably by Dejima militants. Section 9 arrives to defuse the bomb and determine its precise origins.
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.
The Prime Minister is taken into custody, and the military begins its strike on Dejima. The Major and part of Section 9 head to Dejima to try to hand over the nuclear device to the military there, in order to defuse the situation, while Ishikawa heads to SPring-8 to deliver the rest of the plutonium.
Kuze manages to take down the jamming plane, but becomes trapped in rubble with the Major. The Tachikomas begin discussing what to do about the nuclear submarine they have spotted, and Batou manages to convince the special forces that have been sent to kill them to listen to him.
The tables seem to be turning in favor of section 9, but the nuclear missile is still being prepared for launch. The Tachikomas take control of the AI satellite, and take out the nuclear missile.
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