In a near future, technology has firmly taken root into society at large. Cybernetic implants are nothing uncommon and robots roam as plentiful as humans, all connected through their ''ghosts'' to the electronic datastreams of the net.

Major Motoko Kusanagi and the Public Security Section 9 find themselves in a constant battle with the newly created wave of technological terrorists and cyber-hackers. But things take a turn once Motoko gets involved in a certain case involving an extremely dangerous ''ghost''hacker nicknamed the Puppeteer, as she dives deeper and deeper into the limitless reality of the net, to reach her own startling conclusions.