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.

Post Traumatic Stress Disorder is put on full display. A Japanese National named Gino, who suffered through the horrors of Non-Nuclear World War IV, the Second Vietnam War, now passes his days as a helicopter pilot for the chairman of a media conglomerate. His cushy job, however, does not take away the sheer internal pain that Gino is facing.

As he moves through his isolated existence, Gino leaps between reality and fantasy. However, he keeps his dementia solely to himself. Having no one to help him, his condition continues to worsen.

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.

While on an assignment guarding the Prime Minister, Saitou and the Tachikomas pass the time playing poker with a few policemen who are also assigned to the case. Much to the chagrin of the other men, Saitou wins hand after hand.

The Tachikomas take notice of Saitou's uncanny accuracy and start to comment. Their constant chattering quickly gets on the other player's nerves, so to smooth things over Saitou recounts his time working as a sniper for mercenaries in Mexico.

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.

Regrouping, the team decides to refocus the investigation to the events surrounding Kuze. They start a secret investigation into Sagawa Electronics, the company responsible for the nuclear material transaction, and find that Gouda was involved. Meanwhile, as the boat heads for Dejima, Kuze makes his own unsettling discovery.