Motoko is about to be fitted for her new prosthetic body. But when the doctor arrives and begins the procedure, it's clear that she has no intent of letting Motoko out alive. Meanwhile, Aramaki receives a disturbing message that his brother has been kidnapped.

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?

Saito recounts his first run-in with the Major, and how he became part of the group that would eventually become Section 9.

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 tables seem to be turning in favor of Section 9, but the nuclear missile is still being prepared for launch.