Careful choice of faction alignment needs to be considered in some parts of the story, for it may be difficult to progress further if the Stalker who the player is interacting with is hostile, has needed information, or is essential to triggering the next stage.

The Swamp-dwelling Renegades or the Military factions cannot be joined. While Scar is always aligned with Clear Sky, and his ultimate goal is to defeat Strelok, he can fight against or ally with the four other factions in the Zone (Loners, Duty, Freedom, and Bandits). Each of the main factions provide services, most importantly access to a trader and an engineer. The player character is a mercenary, and may do missions for any faction or remain completely neutral without disrupting the necessary progression of the game. The stronger a faction becomes, the better equipment the traders can provide and their soldiers can use. The player will be able to join and help factions in their battles. Different factions will struggle for territory, attacking to gain territory and then defending to keep it, while others then try to retake it. The most significant gameplay addition since Shadow of Chernobyl is the faction wars system.

This game combines elements of first-person shooters ('twitch-based' aiming, with a first-person perspective), survival horror (ammo-scavenging in a frightening atmosphere with powerful monsters), and role-playing video games (inventory management, quests, character interaction, armor types, and defense stats).

Stalker clear sky art