Upon returning to 2010, Renko finds that nothing has changed. He sees Demichev holding Barisov at gunpoint. Demichev reveals that he rebuilt the facility after the bomb detonated. Renko shoots and wounds Demichev, freeing Barisov. Barisov realizes that Demichev's rescue is what altered the timeline, and tells Renko that he must go back in time and warn himself to stop rescuing Demichev. Demichev reveals that Renko already tried that; he was the unidentified man that Renko saw in the fire. Barisov realizes that Renko must kill his past self to stop him from saving Demichev. Demichev offers Renko unlimited power in exchange for the TMD, while Barisov pleads to Renko to travel back in time and kill his past self to stop Demichev. The player is left with the choice of 2 endings as well as two more less-obvious ones.
If the player chooses to kill Demichev, Barisov will still urge the player to go back in time and stop himself from saving Demichev in the fire in order to set history back to normal. The player then assumes the position of the man who shouted at Renko in the fire. The player can choose to shoot Demichev instead of Renko, however this will only repeat the same scene. Shooting the past version of Renko sends the narrative back to Devlin and Renko's arrival at Katorga-12. The game's intro credits are shown written in Russian, the helicopters bear the hammer and sickle on the side, and Devlin, armed with a Russian weapon, comments that monitoring Katorga-12 is a waste of time. The helicopter moves past the statue seen in the introduction, but it has changed into a massive monument to Barisov wearing the TMD. Renko seems to have retained his memories from the rest of the game, as he checks his left hand when he sees the monument. Renko and Devlin's mission is called off by their dispatcher — Red Fleet instead of Titan One — and Devlin refers to Renko as "comrade". It is implied that Barisov recovered the TMD from the fire and used it to unite the world under Soviet rule.
If the player shoots Barisov, he joins forces with Demichev and the team succeed in taking over most of the world, with Renko training the Katorga-12 mutants as soldiers and using them in all of his battles. But with his control of the TMD, Demichev feels Renko is even more powerful than he is and takes precautionary measures against him by starting a weapons research program in the former United States. This settles the world into another Cold War with Renko on one side and Demichev on the other.
If the player shoots Demichev and Barisov, Renko leaves Katorga-12 and allows the world to fall into chaos. The public believes his very existence to be a myth as he disappears with the TMD in his possession. The Singularity explodes some years later and destroys the eastern coast of Russia and the Western coast of Alaska. Katorga-12 mutants escape onto mainland Russia and wreak havoc. A new leader rises in the former United States and is reported to be very aggressive. The ending cut scene and narration imply the leader to be Renko, as it shows an arm wearing the TMD along with the narration stating there are rumors that the new leader has god-like powers.
If the player simply waits for a while, Demichev will grab the pistol on the floor and shoot both Renko and Barisov.
A post-credit scene shows a wounded Kathryn emerging in 1955 from the Pearl's wreckage and hiding in an office. Bleeding heavily, she begins writing the Mir-12 journal