Top Secret is a scrolling platform shoot-em-up set ten years after World War III in which the player takes on the role of 'Super Joe'; an elite Commando tasked with infiltrating the enemy's military base to discover their secrets plans and destroy their missile silos.

Joe is equipped with a bionic arm; a telescopic grappling hook that is used to traverse the many platforms and ledges that make up the game's levels. The arm can also be used to temporarily stun enemies or knock them from platforms, as well as to retrieve the bonus items and weapons that are occasionally dropped in wooden crates by parachute.

As well as the bionic arm, Joe is armed with a shotgun needed to actually kill the enemies. The shotgun can only be fired left and right, however, and cannot be used at the same time as the bionic arm.

The game consists of four levels:
* Level 1: Forest
* Level 2: Enemy Outpost (The Forefront)
* Level 3: Underground Base (Infiltration)
* Level 4: Final Base