Set after the events of Ghost in the Shell 1.5: Human-Error Processor (and presumably before Ghost in the Shell 2) Fujisaku explains he is writing The Human Algorithm as if it were Ghost in the Shell 1.75. The manga focuses on Section 9 following the disappearance of the Major. More specifically, it closely follows the characters of Togusa, Batou, Azuma, Ishikawa and newcomer Tsunagi.