If the character dies, the game continues from the most recent checkpoint. As in the predecessor game Limbo, these deaths are presented realistically and are often graphic. The boy can die in various ways, such as being shot with a tranquilizer dart, mauled by dogs, ensnared by security machines, blown apart by shockwaves, or drowned. If all the orbs are deactivated during a playthrough, the player unlocks the game's alternate ending.

The player controls the boy who walks, runs, swims, climbs, and uses objects to overcome obstacles and progress in the game. The boy gains the ability to control bodies to complete certain puzzles, a mechanic that IGN's Marty Sliva compared to a similar mechanic in The Swapper. At various points in the game, the player may discover hidden rooms containing glowing orbs. The game is also mostly silent, with the exception of occasional musical cues, the boy's vocals, dogs barking, equipment and sound effects. The game is dark, with color used sparingly to highlight both the player and certain parts of the environment. The player character is an unnamed boy who explores a surreal and mostly monochromatic environment presented as a 2.5D platform game.

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