During a visit to the Dejima Refugee Residential District off the coast of Nagasaki, Prime Minister Kayabuki receives a bouquet of flowers that is accompanied by an envelope stamped with the diamond seal seen in "NATURAL ENEMY". The envelope contains a letter that promises an attempt to take the Prime Minister's life. At a meeting of the Prime Minister's Cabinet, Aramaki is shown the letter and told that so far the stamp on the envelope has turned up in eight other terrorist incidents. The Cabinet calls for Section 9's assistance. However, much to the unit members' chagrin, Section 9 will not be deployed in an offensive role.

A highway accident involving a large commercial truck has left a fully prostheticized man dead, his body torn apart from the impact. Togusa is summoned by Aramaki to delve deeper into the matter as the dead man had recently tried to blackmail the Energy Ministry. The dead man's name was Kanji Kotan and he had recently arrived to Niihama by way of Tōkyō. Due to the rest of Section 9 guarding the Prime Minister ("INDUCTANCE"), Aramaki can only send Togusa, with a Tachikoma as protection, to dig up what he can about the man's recent activities before he died.

The year is 2032. Following the events of the first Ghost in the Shell movie, Major Motoko Kusanagi has since left her physical body and is now a "ghost" living in the network. This leaves Batou as the top officer at Section 9, the special task force assigned to matters of human/machine relations. Batou's latest assignment is to investigate the recent string of suicide-murders perpetrated by a certain brand of "gynoids," androids designed to look like women. Together with officer Togusa (one of the last few people who hasn't had his body fitted with cybernetic parts), Batou tracks down the cause of the wayward gynoids — all the while pondering and discussing the hazy realms where machines become dangerously close to human, and humans become dangerously close to machines.

No description available.

No description available.

While Ishikawa begins to dig deeper into the background of CIS Representative Kazunoto Gouda, the rest of Section 9 are instructed to arrest one Shou Kawashima, a Taiwanese vegetarian restaurant chef who has been seen at three locations where the Individual Eleven have claimed responsibility for attacking. The Taiwanese restaurant where he works is near the Nanyou Shimbun (Newspaper) building that had received an earlier threat against it by the Individual Eleven. Section 9 moves into position around the Taiwanese restaurant and commences their stakeout.