Set in 2030, Ghost in the Shell: Stand Alone Complex follows the story of cyborg agents Motoko Kusunagi and Batou as they battle terrorism and crime. Section 9, a secret government agency, is tasked with fighting against these threats.
The gameplay takes place from a third-person perspective, requiring players to fight, jump, and climb their way through twelve missions. Between missions, the story unfolds in full motion video, while communications received during a mission are also displayed. Players can collect various weapons and ammo, as well as hacking keys, which allow them to see enemy locations on screen and control certain enemies' actions.