Yevhen "Skif" Martynenko, a veteran of the Ukrainian Marine Corps, has returned from a 3-year deployment in an unspecified conflict. He awakens to find his apartment has been destroyed by an anomaly that has mysteriously appeared outside of the Zone, leaving an unknown artifact in its wake. Looking to earn money for a new home, he is smuggled into the Zone by a scientist, Professor Hermann, along with a piece of technology called the 'Scanner' that creates local anomalies and can apparently "recharge" depleted artifacts. Venturing into the Zone, he finds his initial team he was to make contact with have been killed and sets out alone to use the Scanner in special coordinates where it works. On the third and successful attempt, he is interrupted by an investigation from soldiers of the faction called 'Ward', dedicated to controlling the Zone and stopping its expansion. The soldiers themselves are killed by an unknown third party, who steal Skif's belongings and knock him unconscious.
Skif awakens and sets out to recover the Scanner and artifact, aided by a friendly loner named Richter. He finds himself on the trail of Solder, who sold him and the scientists the coordinates of where to place the Scanner, collaborating with either the local Stalkers or the Ward in the process. Following the trail, he is led to Scar, the protagonist of S.T.A.L.K.E.R.: Clear Sky, who leads an anarchistic faction called Spark that opposes the Ward and believes the Zone can be transformed into a utopian 'Shining Zone', as well as the Noontide faction, consisting of the formerly-brainwashed soldiers of the Monolith from previous games, who seek to make their own lives, having no memory of their pre-zone life or enslavement to the Monolith. They are divided between Strider, who aims to make the Zone a safer place, and Faust, who still preaches the original mindset of the Monolith.
