Mr. Shifty is experienced from a top-down perspective. The player assumes the role of a thief, Mr. Shifty, who is attempting to steal a plutonium core from a building secured by many enemy guards. Shifty advances through a linear series of rooms to reach the end of the stage, which is an elevator on all but the last stage. He must either defeat all the enemies in a room to unlock the door to the next, or travel to its exit while avoiding all its hazards.
Shifty’s signature ability is “shifting”, which teleports him a few meters and lets him pass through thin walls or dodge bullets. Shifting is limited: one shift regenerates for every second the player does not shift, but if the meter is depleted by shifting five times without allowing a recharge, the player cannot shift for five seconds. Some rooms have “shift blockers” that cannot be shifted into or out of. The player can punch to kill enemies in two or three hits, depending on the enemy. Scattered around levels are various melee weapons and items which kill enemies in one hit; these items may be held or thrown, and break after a few uses (except for certain throwable items).
Enemies carry many different weapons, including shotguns, flamethrowers, and rocket launchers. Any hit from a weapon — or from an environmental hazard such as lasers, mines, or turrets — will kill Shifty and send him to the beginning of the room to try again.
Killing enemies adds to a meter at the bottom of the player’s screen, which begins to drain after not killing an enemy for a short time. When this meter is full, the next bullet that comes close to Shifty will activate “Slow-Mo”. During Slow-Mo, shift recharges almost instantly and time is slowed down for all enemies.