In a briefing, Aramaki shows a photo of a girl who looks like Eka Tokura, the daughter of Tokura Electronics, who was kidnapped 16 years ago. But there's one problem–the photo was taken two days ago!

While at an international police conference in London, Aramaki drops by to visit an old flame who's now in the wine brokering business. She asks him to help her put a stop to the corruption in her company, but he tells her that it's out of his jurisdiction. Just then, however, two thieves break into the building and take them hostage.

Despite their best efforts, the remaining members of Section 9 are rounded up one by one by the government forces; only Batou and Motoko are left.

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 hacker and thief by the name of Cash Eye plans on infiltrating a vault during a party, and Section 9 is called in to prevent it. But there are a number of strange elements in this case that don't all add up.

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.

The Tachikomas, Ishikawa, and Borma locate a suspicious file believed to be the Individual Eleven virus, The Major, Batou, Saito go after Kuze, and the Individual Eleven prepare to put their plan into action.

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 and Batou are flown to Berlin in an effort to track down a terrorist called "Angel's Feathers". While there, Batou attracts the attention of a young girl in a wheelchair.

Despite close scrutiny by the authorities, the Dejima refugees declare their independence. Kuze is suspected to be the mastermind behind this new resistance and Section 9 is sent to detain him.

Much to the chagrin of Batou, Motoko, and the rest of the team, Kuze and the refugees manage to escape in one of the camouflaged boats. They are further hampered when an explosion causes heavy losses, leaving them unable to follow the fleeing boat.

The city of Fukuoka is evacuated when a live nuclear bomb is found. With the Dejima Refugees targeted as the prime suspects, the government sends the Self-Defense Forces into the city.

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.