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.
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.
A seemingly run-of-the mill hit-and-run turns into anything but when Togusa investigates. While in Tokyo, he discovers a secret from the past the GSDF is trying to keep hidden deep underground.
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.
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.
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 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.
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