Ghost in the Shell is a 3D shooter based on the original comic by Masamune Shirow rather than Mamoru Oshi's film. The story is set in the future and focuses on a team of policemen led by the female cyborg Major Motoko Kusanagi, which fights technology-related crimes. The player takes the role of a new member in Kusanagi's anti-terrorist squad and gets to accomplish missions on the Fuchikoma, a spider-like AI equipped tank. During the course of the twelve missions a plot starts to surface concerning a giant skyscraper, the Aereopolis II.

The Fuchikoma can be controlled from either third- or first-person view. It is permanently equipped with a machine gun, homing missiles (which are activated by holding the attack button), and limited supplies of grenades; there are no other weapons or tools in the game. The Fuchikoma can also jump, strafe, stick to the walls, climb on them, and even move on the ceilings. Missions mostly take place in enclosed outdoor or indoor areas and often involve destroying specified targets. Two of the missions are rail-shooting sequences.