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.

Batou goes undercover on a military base to shadow one of his former heroes, a man named Zaitsev who was an Olympic silver medalist. Now, however, he's under suspicion of espionage. Batou befriends him easily, and the two really seem to get along--which is unusual for Batou. But when Batou learns the truth behind his hero, he must make a very difficult decision.

Togusa has been released from jail and he's given papers showing the dissolution of Section 9. Out of work and depressed, he tries to find information on the others, but there is nothing available. Thinking that he has nothing left to lose, he goes to assassinate the man responsible when he is stopped by–Batou!

The tables seem to be turning in favor of Section 9, but the nuclear missile is still being prepared for launch.