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.
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.
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.
Public Security Section 9 is an elite special ops unit that works directly under the control of the Prime Minister. They've been called in to rescue a high-ranking government official from a hostage situation. But something doesn't seem right to Major Motoko Kusanagi. After some investigating, Section 9 uncovers a major espionage plot, and it's up to them to prevent a major international incident.