After a fierce chase involving the Fuchikoma, Kusanagi and Togusa apprehend the suspect. Meanwhile, while Aramaki and Batou stake out the location, the unidentified hacker known as "The Puppet Master," who is suspected to be the one who planted the virus, makes an appearance at Colonel Mares's location.

Kusanagi and her team head to the northernmost point to monitor the combat cyborg Coil Krasnov. To uncover Coil's objectives and the corruption hidden behind Sagawa Electronics' expansion of the underground factory, Kusanagi heads to Sagawa Electronics headquarters, while Batou and his team head to the underground factory.