Marco Amoretti, a former Navy Petty Officer from the American Empire, has come to Japan and is committing heinous acts of brutality against women.

Section 9 is assisted in this matter by the American Empire's CIA. While this doesn't sit well with Public Security's members, Batou finds the whole case particularly hard on his psyche as the nightmares from his past rear their ugly head.

After the events of "MACHINES DÉSIRANTES", the Tachikomas are sent back to the lab for further testing. Batou has little time to ponder the loss of his pet, however.

A foreign spy is suspected to be working within a Japanese Self-Defense Force training camp based in New Port City. With the Major and the Chief away at a security conference in England, Batou alone is assigned to go undercover to confirm the suspect.

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.

Kuze and the Major come up with a plan to save the refugees, but the chances of its success are slim. Realizing this, the Tachikomas disobey the Major's orders and come up with a plan of their own. Batou has also disobeyed the Major's orders to go to the bridge and is desperately searching for her in the ruins of Dejima. Meanwhile, the Prime Minister is frustrated with being spurned by the Chief Cabinet Secretary. Determined to be remembered as more than a mere figurehead, she takes matters into her own hands.