The nature of these changes becomes clear shortly. It is not known how Scar has survived the emission, but it is noted he has suffered damage to his central nervous system and seems to exhibit other, subtle physiological changes. Scar, the only one to survive, is then rescued by Clear Sky, a secret independent Zone faction dedicated to researching and learning about the Zone in their attempt to better understand it and its related phenomena. While guiding a group of scientists through the Zone, Scar faints during a high energy emission. If not adequately concealed, the player's nervous system shuts down, resulting in the player's death. Emissions also occur on an infrequent basis, requiring the player to take cover in a building or underground area pointed out by the PDA.

Emissions, powerful waves that are sometimes visible or invisible (determinant by intensity), unleash lethal radiation, psi-emissions, and other unknown particles and energy directly from the Chernobyl Nuclear Power Plant, directly affecting the Noosphere in The Exclusion Zone, making it deadly to all lifeforms except specific mutants. There are guides in the zone who will provide fast-travel for a fee. Non-player characters are given the ability to use hand grenades, take cover dynamically, and use 'blind-fire' techniques. Anomalies are harder to notice and now contain the artifacts in the game, which require a detector to locate. Other gameplay advancements since the first game include a deepened weapon customization system with the ability to repair damaged gear and add modifications that improve weapons and suits. 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 call of chernobyl factions