The game continues the story depicted in Manhunter: New York. The game begins with the player, piloting an Orb ship in pursuit of the antagonist Phil Cook, crash-landing in San Francisco. Another manhunter on the ground is killed in the crash, so the player assumes his identity. As the gameplay progresses, the player learns of an organized resistance, experiments that have created mutant slaves, and the goal of the malevolent Orbs. The game reaches its climax at the end when the player is on the verge of catching Phil Cook who escapes in an Orb Ship with the player hangs on to the outside, flying off towards London where the third and final game is to take place.
Each game uses different controls, most DOS games use the keyboard arrows. Some will use the mouse , "Alt" ,"Enter" and "Space bar".