In Nachtmission you play as the pilot of a rescue helicopter. You begin at your base and fly into enemy territory to rescue the prisoners there. When a prison is found, you must shoot a hole in the wall to release the captives. Once you've collected some prisoners, you must fly them back to your base and drop them off. Your helicopter can only hold a limited number of captives at once, so you must make several trips. There are tanks in your way at the start, and as the enemy becomes aware of your efforts, jets and drones appear to add to the difficulty. Prisoners can easily be killed by friendly or enemy fire, or by landing on them. The objective is to rescue as many prisoners as possible while losing as few helicopters as possible.

The world is 2.5-dimensional: it is presented in 3D but the player can only move up, down, left, and right. The player can rotate the helicopter in different directions: facing forward, the helicopter shoots straight down, making it easier to hit targets on the ground. Facing left or right, the helicopter shoots in those directions, which is best for hitting airborne targets. The helicopter can fly in any of the four directions independent of which direction it is facing.