After the attack on D6, Artyom becomes disillusioned with the constant infighting and corruption within the Metro and leaves the Spartan Order. He soon becomes obsessed with proving that other human survivors exist outside of Moscow and makes numerous dangerous expeditions to the surface, much to Anna's concern and Miller's frustration. However, on one such expedition with Anna, they witness a working train running on the surface. Before they can follow it, they are captured by Hansa soldiers, along with a group of people who claim to be from outside of Moscow. The Hansa soldiers execute the other prisoners, and Artyom is shot and left for dead, taking Anna to their base. Surviving the gunshot, Artyom follows the soldiers to rescue Anna, and in the process inadvertently destroys a signal jammer that was blocking all communications going in and out of Moscow. Radio transmissions from all over the world begin to be picked up, and Artyom and Anna realise humanity has not gone extinct. They escape by stealing one of Hansa's locomotives, the "Aurora", with the aid of a defected Hansa train engineer called Yermak.

As the train leaves, the Spartan Order moves in to retake it and are shocked and confused at Artyom and Anna's presence. Knowing that Hansa will have all of them put to death for knowing the truth, Miller concludes that the Spartans' best chance of survival is to flee Moscow. Once outside the city, he reveals to the others that while many of Russia's cities were bombed, the war did not end and NATO proceeded to occupy what was left of the nation. To prevent NATO from attacking Moscow, the Russian leadership decided to secretly jam all communications to make the outside world believe nobody had survived. They then receive a radio broadcast from Moscow Defense Command calling for survivors to rally at the "Ark", located at Mount Yamantau. Miller decides to head there, believing that the Ark is where the Russian government has rebuilt itself.

After crossing the cult-controlled Volga River, the Spartans reach the Yamantau base. They discover the base's service and construction crew have devolved into cannibals who lure survivors in with the false promise of safety. Artyom and the Spartans manage to fight their way out and escape, but Miller's faith in Russia is shattered when he discovers that the government never took refuge in Yamantau, nor survived the war, and thus the Spartans are left wondering what to do next. Using a map they recovered from Yamantau, they decide to travel to a satellite communication center near the Caspian Sea in the hopes of gaining access to a satellite to find habitable land to settle. At the dried up remains of the Caspian Sea, the Spartans steal water and fuel from the local bandits while obtaining an updated satellite map.

As the Spartans continue on their journey, Anna begins to cough up blood, fearing the cause was accidentally breathing poison gas during the journey. They decide to scout a nearby taiga forest valley to see if it is suitable to settle. While scouting the forest, Artyom is caught between two rival survivor factions, and he discovers that the dam protecting the valley from radiation is on the verge of failing, making the area uninhabitable. Artyom returns to the train to learn Anna's condition has worsened. The Spartans detour to the heavily-irradiated city of Novosibirsk, the closest location where an antidote may be found.

Miller and Artyom decide to head into the city alone to search for the antidote despite the risk. They enter the Novosibirsk Metro and find a young boy named Kirill, one of the last of the Novosibirsk survivors, who explains that his father left on a mission to obtain a map marking the location of a clean, habitable area. Miller and Artyom split up, with Miller going to find the map and Artyom searching for the antidote. He manages to recover the antidote, but is gravely wounded by a mutant and absorbs a heavy dose of radiation. Artyom, Miller, and Kirill return to the train with the map and the antidote, but Miller dies of radiation poisoning on the way back after using a dose of anti-radiation serum meant for himself to save Artyom. The rest of the Spartans donate their own blood to give Artyom a critical blood transfusion. Anna is cured with the antidote and with the map, the Spartans settle on the shores of Lake Baikal, which is completely free from radiation.

Artyom's ultimate fate depends on the choices the player made during the journey; In the bad ending, Artyom dies from the radiation poisoning, and the Spartans and a grieving Anna hold a funeral for him and Miller while Artyom's and Miller's spirits awaken on a dilapidated version of the Aurora, remaining in the ghostly purgatory for eternity. In the good ending, Artyom survives. Miller is buried and Artyom is selected to take his place as leader of the Spartan Order. Now with a home free from radiation, Artyom decides to return to Moscow and reveal the truth of the world to the survivors of the Metro.