S.T.A.L.K.E.R.: Clear Sky is a stand-alone prequel to the original game of 2007. This game takes player back to the anomalies ridden territory surrounding the dormant Chernobyl nuclear powerplant called the Zone. The story of Clear Sky is set one year prior to the events unfold in the original game. Assuming control of the stalker named Skar the player finds himself subjected to lethal dosage of nuclear emission and surviving. The game begins its narrative by challenging player to uncover the truth behind his condition and find the true source of those emissions. The player will the return to the already familiar locations, even though they aren't exactly what player may remember of them from the original game, as well as explore new areas and meet new characters.

Gameplay-wise the game has benefited from a modified quest system which now closely follows his relations with the faction. At one point or another the player may choose to become involved in one of the faction wars (by joining one of the factions). These are the full-scale events which challenge player to capture a number of points in order to weaken the enemy faction presence in the region. Thanks to the modified AI of the game, the stalkers of your faction won't wait for you to do their jobs. In fact, they may complete all of the objectives without you. However, since your reward will reflect your involvement in the battles, it is not advisable to loiter.

Another distinct change is artifact hunting. Before, artifacts were frequent and visible to the naked eye. Now, artifacts are rare and need to be 'detected' using a scanner which will locate nearby artifacts and will appear when the player is close enough, often in situated dangerously close to surrounding anomalies. Artifacts now also have slightly different abilities and different armor has limited artifact slots that may be equipped.

A lot of changes were made to S.T.A.L.K.E.R.'s appearance as well. The game's in-house developed X-Ray engine has learned to support full dynamic lightning with every single object casting soft stencil shadows on the normal mapped environments. The game now supports DirectX 10 enabled features like softer shadows, volumetric fog and light and wet surfaces. The in-game models were also reworked to include both an increased polygon count and a normal map.