Kusanagi and her boyfriend are rushed to the hospital after being attacked without warning. They suspect Toru Soma, a terrorist that Kusanagi has a history with. Kusanagi and Togusa leave the hospital, and after leading their pursuers on a chase, they find themselves in a fierce battle against an armed group in an abandoned factory. 

After diving into the Puppet Master's world, Kusanagi awakens. The truth of the incident is revealed, but Kusanagi occasionally senses the Puppet Master's presence. In one operation, the Ghost in the Shell team subdues terrorists on a ship, but Kusanagi accidentally shoots and kills the leader.