A group of terrorists identifying themselves as the Individual Eleven barricade themselves within the Chinese Embassy. Section 9 is called in to eliminate the terrorists before the scheduled police raid.
A refugee living in Japan has plans to reset the world and change things. But are his plans merely violent daydreams, or something more sinister?
A thief plans on infiltrating a vault during a party and Section 9 is called in to prevent it.
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; a mysterious man known as Gohda arrives to tell Section 9 how to handle it.
Assassination threats against the prime minister, who has revoked the Refugee Special Action policy, bring in a reluctant Section 9 protection unit.
Togusa investigates a seemingly run-of-the mill hit-and-run; while in Tokyo, he discovers a secret from the past the GSDF is trying to keep hidden.
After secret plans to ship plutonium are leaked, the Prime Minister orders Aramaki to enlist Section 9 to stop terrorists from stealing the material.
The Tachikomas and the Major continue to investigate Gohda; the rest of Section 9 are out to stop a string of suicide bombings.
Togusa is brought up on murder charges.
The Major finds herself hacked; an old woman tells a story from her past.
The Tachikomas locate a suspicious file.
The group tracks down the designer of Kuze's face.
Saito recounts his run-in with the Major.
The Tachikomas discuss individuality.
The Prime Minister learns about hub cyberbrains; Iskikawa returns from the peninsula.
The Major investigates a lead on Kuze in Taiwan.
Batou and the Major are sent to Berlin in order to track down the Angel's terrorist wing.
The Major hacks the refugee cyber brain hub to determine Kuze's location.
Section 9 is alerted to Kuze's true location.
Kuze escapes, leaving Section 9 with severe damages as a result.
The entire city of Nagasaki is evacuated and the JSDF is summoned after a live nuclear bomb has been planted in the city.
The government declares martial Law in Dejima, believing that the refugees have a nuclear device they plan to use.
As the Prime Minister is taken into custody, the military begins its attack on Dejima.
Kuze manages to take down a jamming plane, but is trapped in rubble with the Major.
The Tachikomas take control of the AI satellite and take out the nuclear missile.