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 botched arms deal reveals that the government's plans to remove Plutonium from the Shinjuku dig site ("EXCAVATION") by sea have been compromised. Section 9 is called in to take the Plutonium out of Old Tōkyō by land.

The members of Section 9 are not happy being used by the government. Batou is especially incensed since Section 9 is supposed to be an offensive organization. His patience will be further tried when he and Section 9 find out who will be accompanying them on their mission...

Togusa aids a woman who has been chased by a man through the streets of Niihama. With his Mateba, Togusa is able to disable the man's prosthetic body. However, he does not secure the man's pistol. When Togusa helps the woman up, the man has enough movement left in his body to aim his gun and fire at the woman, killing her instantly.

The murderer is brought to trial. However, due to the events that occurred immediately following the murder, Togusa is brutally cross-examined by the murderer's lawyer.