Pilot Down: Behind Enemy Lines is set during WW2, focusing on the story of an Allied airman who must navigate through enemy territory to reach the safety of Switzerland. The player takes on the role of this man, trying to evade detection by German troops while making his way through levels featuring various environments.
The gameplay involves sneaking around and avoiding detection in environments such as a lumberyard, wilderness, and others. The player can use objects like cigarette packs to distract guards or apples to replenish stamina. However, the player character has limited stamina, which depletes when exposed to cold water for too long. To restore stamina, the player must warm up by campfires or eat occasionally.
The game also features a variety of weapons that can be used to dispatch enemies who get too close, including items like piano strings and machine pistols.