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.

Togusa is on the trail of the Laughing Man again, and this time, his investigations lead him towards both a leading micromachine corporation and an NGO called the Sunflower Society.

The Laughing Man returns! And, just as he did six years ago, he kidnaps the president of Serano Genomics without being detected. Section 9 arrives at Serano's house too late, and sets out to find him.

While field testing new recruits, the Major finds herself hacked, and an old woman tells her a story from her past.

Section 9 heads to Etorofu in search of Kuze. During their investigations, the Major finds an interesting floppy disk on the body of a dead addict.

Kuze manages to take down the jamming plane, but becomes trapped in rubble with the Major. The Tachikomas begin discussing what to do about the nuclear submarine they have spotted, and Batou manages to convince the special forces that have been sent to kill them to listen to him.