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.

Togusa has been released from jail, but his badge and gun are confiscated and he is given papers showing the dissolution of Section 9. Out of work and depressed, he tries to find information on the others, but turns up nothing.

Trying to turn his life around, he begins to look for a new job, only to be sidetracked by the ongoing case against Secretary-General Yakushima involving the illegal use of micromachines. With the news plastered everywhere, Togusa cannot help but wonder where he stands now.

A joint training exercise between the Japanese Ground and Maritime Self-Defense Armies that takes place within the sealed sector of New Port City's Refugee District goes awry, putting the Asian refugees in danger. Section 9 Chief Aramaki takes the matter up with Kubota, his friend at the Ministry of Defense.

While there, Aramaki is approached by a man from the Cabinet Intelligence Service: Kazunoto Gouda. Acting as a representative for his superior, the Chief Cabinet Secretary, Gōda requests that Aramaki bring the full force of Section 9 to bear on the situation. There's just one catch...