As Agent 006, you are the world's only hope: the terrorist organization known as the D.V.S. has captured the blueprints to a new, powerful weapon known as the "Red Rock Rover". Your mission is to infiltrate several islands occupied by the D.V.S. and retrieve each part of the blueprints. The shareware version only has the first episode available, the registered version consists of three installments, packed as separate executables.

Secret Agent is a side-scrolling platform game, where your objective is to complete 15 levels, allowing you to gain access to the "main fortress" which is the 16th level. On each level, you have to find and destroy a radar dish, and also find a bundle of dynamite and place it at the exit to blow it open.