A certain type of android, the GA07_JL, nicknamed Jeri by its users, has been affected by a virus. Recently, all Jeri model androids have been committing "suicide". Section 9 is called in as it may be related to a virus detected in an android at the National Assembly Building.

One of the Tachikomas decides to take a little stroll through the city. It meets a little girl, Miki, who is searching for her lost dog and it agrees to help her. On their journey, the Tachikoma finds a strange box.

Section 9's next case is a rash of mass-kidnappings. Rumor has it that a crime syndicate is harvesting organs and selling them on the black market. As they research the case, they realize that time is running out.

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?

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