Kusanagi and her team begin operating as the Ghost in the Shell unit after being scouted by Aramaki. One day, a virus infiltrates the cyberbrain of the Foreign Minister's interpreter. Sensing that Colonel Mares, who is in exile, is trying to disrupt a secret meeting, Aramaki instructs Kusanagi and the others to track down the culprit using reverse tracking.

There has been a rash of attacks against humans by promotional sample robots. Kusanagi's team rounds up robots of that same model line, and they learn that they all share a common trait. Batou and Togusa head to Hanka Precision Instruments, where they are made, to determine what is behind the attacks.