You are a secret agent sent to infiltrate and enemy base and take out their leader. Armed with your fists, a knife and a pistol, you will have to defeat all enemy soldiers you encounter and rescue any trapped scientists.
The Super Spy is played from a first-person perspective. The actual graphics are done using two-dimensional backgrounds and sprites, but are arranged in such a way so that you view the world from your character's eyes. You can scroll left and right through hallways and enter any doors you come across by pressing forward. You can also walk forward into any vertical hallways you encounter to get to horizontal hallways further in the background. The game consists of a series of levels, all laid out as mazes with horizontal and vertical hallways to traverse.