Events begin to shift into overdrive after the events of "ERASER". While things seem to be going Section 9's way, people in the shadows are starting to appear.

As Motoko, accompanied by her friend Kurutan, arrives at the hospital to switch to a new prosthetic body, Togusa begins the recovery process after being wounded by the DEA's NARC Squad. However, the people still active within the NARC Squad have a few more surprises in store.

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...