Following nuclear World War III and non-nuclear World War IV (also referred to as the Second Vietnam War), Japan passed an act known as the Refugee Special Action Policy, inviting war refugees from all across Asia to enter Japan.
The largest live fire exercise ever conducted by the Japanese Self Defense Force is currently underway in advance of the Prime Minister's planned announcement of the repealing of the Refugee Special Action Policy.
The prime suspect behind an attempt to blackmail the Ministry of Energy has turned up dead in Nihima City. Originally presumed to be a victim of a tragic accident; however, a more thorough examination of the body turns up evidence of homicide.
Tired of being manipulated by Gohda, Aramaki decides to take the initiative and conduct his own investigation on the Individual Eleven case while simultaneously looking into the Cabinet Intelligence Agency.
The failed attempt to secure the ex-GSDA officer for questioning has proven to be the straw that breaks the camels back, as Major Kusanagi decides to go directly into the Cabinet Intelligence Agency database to determine what Gohda is up to without all the added wires and strings.
The Tachikomas locate a stealth gate that can only be accessed through the European Satellite system. After passing through the gate, Boma recovers a suspicious file believed to be the virus that infected The Individual Eleven.
Representatives from the American Empire have arrived in Japan to discuss a new security treaty and Section 9 is one of the various groups assigned to secure the building where the talks are taking place.
Section 9's Tachikoma fleet is down for routine maintenance. While the technicians inspect the fleet, the think tanks begin a philosophical discussion on the Individual Eleven case and the implications and motives behind it.
Batou confronts Kuze in an effort to stop him from leaving with the plutonium, but Kuze proves to be a better fight than Batou and ends up disabling Batou's right leg and left arm and putting Batou out of commission.
A tactical nuclear device has been discovered in the Kyushu Telecom Tower in the Japanese capital of Fukuoka and some 35 million citizens are subsequently evacuated over a five-day period to allow the Ground Self Defense Army to safely diffuse and remove the device.
Prime Minister Kayabuki meets with her cabinet to discuss the Fukuoka nuclear bomb incident, but the cabinet has already decided to deploy the army to retrieve the remaining plutonium supposedly hidden on Dejima Island.