The story of S.T.A.L.K.E.R.: Clear Sky brings the players one year prior to the events of the original S.T.A.L.K.E.R. game in 2011.

A group of stalkers has for the first time reached the very heart of the Zone - Chernobyl Nuclear Power Plant, and brings about a cataclysm on the brink of a catastrophe. An immense blow-out of anomalous energy changes the Zone. There are no more reliable and relatively safe roads. The entire levels vanish in the outbursts of anomalies. Stalkers and even expeditions die or end up sealed on the lost territories. New areas, which remained unknown since the time of the Zone emergence, appear on the Zone map. The Zone continues to shake with blowouts. The Zone is unstable. The anomalous activity is at its maximum.

Changes of the Zone map known to stalkers shake the fragile balance of forces in the Zone. Among the groupings, there flare up hostilities for the new territories, artefact fields and spheres of influence. There are no more old enemies or friends - now everyone is for himself. The Factions War has started between the groupings.