The Swapper is a puzzle-platform game with a side-scrolling perspective. In the game the player has control over "The Swapper", a device that allows the player to create clones of him/herself and take control of them (swapping). All clones respond to movement input, but only the active clone can activate buttons and create new clones. Puzzles consist mostly of trying to move the different clones to the correct position at the right time so that door are opened by the pressure plates they can stand on. Additional difficulty arises from red, blue and purple lamps which block the player from swapping to other clones, creating new clones or both respectively.
The game takes place on an mostly abandoned space station. Its story unfolds mostly through diary logs and encounters with an NPC. Thematic to the story is cloning in relation to human consciousness and the soul.