The player takes the role of Marine Captain Jonathan "Jon" North, who, along with his brother Robert, is sent to the Russian-Ukrainian border to destroy an abandoned stockpile of Soviet-era bio-weapons before they're stolen by terrorists. The two succeed in their mission, but are ambushed by an unidentified group of special forces soldiers, led by a man named Vasilisk who plays a game of Russian roulette with Jon before knocking him out and capturing Robert. Two years later, Jon is sent to Georgia to help destabilize the local Georgian Separatist cells, who are reported to be receiving an abnormally high level of funding and resources. Jon accepted the assignment with the hidden agenda of locating his brother Robert, after hearing intelligence chatter placing him in the region. He is assisted by his JSOC handler Frank Simms, a Georgian Loyalist ex-special forces sniper named Lydia with whom he was formerly in a romantic relationship, and Israeli Mossad agent Raquel, who is in the region looking to capture and recruit a Russian scientist named Sergei Flostov whom she believes is being held by the Separatists. The Separatists are led by a pair of twins, Davit and Tomas, and a woman named Inna, whom Tomas is scheduled to marry. Jon infiltrates the wedding in hopes of gathering intel to help him assassinate Tomas later, but the wedding is interrupted when Tomas' bodyguard guns him down at the altar before being killed himself by an unseen sniper. Continuing other missions against the Separatists, Jon learns that events in Georgia are being manipulated by an international conspiracy known as the 23 Society, whose forces are equipped with high-tech experimental weaponry and led by a mysterious soldier with seemingly superhuman abilities known as Armazi. In the process of destabilizing the Separatists, Jon is sent to kill a local crime lord doing business with the Separatists, who turns out to be Vasilisk, who is revealed as a member of the 23 Society. When confronted by Jon, Vasilisk once again plays a game of Russian roulette with him, which ends with Vasilisk shooting himself in the head before Jon can interrogate him. Jon is eventually confronted by Armazi himself, who turns out to be Robert, who has been subjected to drug therapy, genetic engineering, and brainwashing to transform him into a super-soldier loyal to the 23 Society. Robert demonstrates his superhuman abilities to Jon before unsuccessfully attempting to recruit him into the 23 Society. Later, Jon receives intel that the scientist Sergei Flostov is being held at a Separatist facility. Jon rescues Flostov, who states that he was forced by the 23 Society to help them create brainwashed, genetically modified super-soldiers. Flostov informs Jon that the 23 Society recently captured an American soldier and are going to execute him soon due to failing to brainwash him. Jon travels to the location where the captured soldier is being held and discovers it is Cole Anderson, the protagonist of Sniper: Ghost Warrior 2. Cole, who was defeated in combat by Armazi and later mutilated by him beyond the point of recovery, reveals to Jon that Flostov is actually the leader of the 23 Society, and then asks Jon to leave behind his pistol so that he can end his own life and die with dignity, which he does as Jon leaves to pursue Flostov. Flostov contacts Jon over the radio and gloats about how the 23 Society killed Robert's wife Milla, then used her death to break his mind and brainwash him. Jon saves one of the Separatists leaders, Inna, from an attack by 23 Society super-soldiers, and learns from her that the other remaining Separatist leader, Davit, is allied with the 23 Society and responsible for killing her fiance Tomas. Jon kills Davit, and in exchange Inna tells him where to find Flostov and Robert/Armazi, who are located at an old uranium mine where Flostov has set up a nuclear reactor to produce yellow cake uranium for the creation of nuclear weapons. As Jon infiltrates the mine fighting through mercenaries and 23 Society super-soldiers, the nuclear reactor becomes unstable. Jon confronts Flostov and Robert at the reactor, revealing to Robert that Flostov and the 23 Society killed his wife Milla, staging her death to make it look like she was killed in an American drone strike to turn him against his country. Upon learning how he had been brainwashed and manipulated, Robert kills Flostov, then locks himself in the reactor room to manually stop the meltdown in order to give Jon time to escape, dying of radiation poisoning in the process. Jon exfiltrates in a helicopter alongside Lydia and Raquel, vowing revenge against the remaining members of the 23 Society.