In an alternate version of the present, Tokyo has been decimated by a shocking terrorist attack, and the only hint to the identity of the culprit is a bizarre video uploaded to the internet. The police, baffled by this cryptic clue, are powerless to stop the paranoia spreading across the population. While the world searches for a criminal mastermind to blame for this tragedy, two mysterious children - children who shouldn't even exist - masterfully carry out their heinous plan. Cursed to walk through this world with the names Nine and Twelve, the two combine to form "Sphinx," a clandestine entity determine to wake the people from their slumber - and pull the trigger on this world.

The story follows Motoko Kusanagi, a highly skilled member of the military, whom upon meeting Daisuke Aramaki, a current chief of the Public Security Section 9, in less than desirable conditions struggles to clear her name whilst forming her own independent team with the highest priority under the sponsorship and guidance of the chief Aramaki himself.