Posing as lovers on vacation, Motoko and Batou work to try to stop a terrorist organization whose symbol is the Scrasath. Meanwhile, Togusa investigates a murder of a man who possessed a prosthetic leg manufactured by the Mermaid’s Leg corporation.

Freed of her responsibilities with the 501 Organization, Motoko Kusanagi must now learn how to take orders from Aramaki. Someone hacks the Logicomas, and Batou enlists the help of former army intelligence officer Ishikawa and former air artillery expert Borma. Kusanagi also seeks to enlist ace sniper Saito and undercover cop Paz into the new Public Security Section 9.