You play as Golgo 13 aka Duke Togo, ace sharpshooter and assassin. Based off a character of various manga comics, Golgo is a down-to-business man at the end of a gun. Stuck in the world of espionage among such groups as the FBI and the CIA, Golgo is constantly in mortal danger, and a lethal weapon in his own right.

The Mafat Conspiracy is the sequel to the NES game Top Secret Episode. In this chapter, Golgo must track down a missing satellite from the SDI laser defense system, as well as rescue a top scientist and stop those who would use the satellite for blackmail and terror on the world's nations.

While Golgo is outdoors, the game is a side-scrolling romp where the player can fire and jump. This changes when Golgo enters a building, at which point the game switches to a first person 3D maze. Navigating past soldiers and between floors, Golgo collects various clues to advance the storyline. There is also a driving sequence, and several sniper sequences in which precision aiming is required.