After an endless fall through powerful magnetic storms... you awaken. Your memory erased, you start exploring the world around you. Someone or something is pushing you higher and higher. Suddenly, you spot the most gigantic Tower emerging from the mists. You soon understand that to get the answers to your questions... you have to climb its summit.

The games take place in the year 2030, between the stories told in Ghost in the Shell: Stand Alone Complex and Ghost in the Shell: S.A.C. 2nd GIG. In the year 2030, cybercrime, espionage and terrorism plague a society lost between humanity and technology. As one of the trusted members of the government organization known as Section 9, Major Motoko Kusanagi must uncover the truth behind a mysterious case known only as T.A.R.

Dealing with similar concepts to other incarnations of Ghost in the Shell, the game has an original storyline which follows on from and refers to the PlayStation 2 game's plotline.