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The story, told in the style of a first-person narrative, is recounted by Artyom, the protagonist, as he writes it down on an antique typewriter. Orphaned as a child, he was born just days before a devastating nuclear war of unknown cause obliterated modern civilization, leaving at least 40000 survivors in a charred, ruined wasteland. Moscow, where the game takes place, was reduced to ruins, and those who survived did so only by hiding in its metro system. At the beginning of the game, Artyom, then only twenty years old, is ascending from the metro system with an older man named Miller, the leader of an elite group of individuals known as Rangers - hardened soldiers who are tasked in the safeguard of the Metro. They emerge in the ruins of Moscow, just a short distance from Ostankino Tower, where they regroup with two other Rangers. However, the encounter is cut short by the sudden appearance of a huge pack of strange, hideously mutated rat-like creatures (Nosalises). The party defends itself from the monsters, but is overwhelmed by attacking flying monsters (demons). Shortly after, Artyom is charged by one of these creatures, and the screen fades to black.
The game then abruptly shifts back to eight days prior the battle near Ostankino Tower, with Artyom waking up in Exhibition Station, his current home station, where he was brought as a child by his stepfather, a man named Alex. With him, he is introduced to another Ranger, a man known only as Hunter, with which he fights off a sudden attack of mutated creatures. They are not, however, the real threat, and as Alex explains, said threat comes from the Dark Ones - mysterious alien-like creatures resulted from unprecedented mutations of then-ordinary human beings, apparently capable of driving people insane with their mere presence or of slaughtering groups of armed men with ease. Hunter embarks on a mission to try and find out more about these creatures, and possibly eliminate them. But before leaving the station, he gives Artyom a Rangers' dog tag, instructing him to go to Polis - the most powerful, friendly inhabited station of the entire Metro - and seek help from the Rangers.
Artyom's quest begins when Hunter fails to return, and the young man embarks on his journey to Polis. From Exhibition, he travels to Riga Station and then Market Station. To get to Riga Station, he is hired as a guard for a trade caravan heading that way. Little to their knowledge, the usual way to Riga Station is blocked due to a cave-in, so they must take a service tunnel. This is the first time Artyom encounters the Dark Ones. They make it to Riga Station, and Artyom travels to Market station. He meets a shady criminal named Bourbon. Bourbon enlists his help for a perilous journey through tunnels controlled by brutal bandits and the dilapidated surface of Moscow (known as the "Dead city"), where deformed abominations roam freely. After this dangerous trip, Artyom and Bourbon return to the Metro, but Bourbon is captured while trying to sneak into a bandit-controlled station. Forcing his way through the bandits, Artyom witnesses a bandit and Bourbon kill each other, and is then surprised by the sudden appearance of a mysterious and spiritual man named Khan.
Traveling with Khan, Artyom explores some of the most dangerous places of the Metro, abandoned tunnels where no one, neither bandits nor animals dare venture. These tunnels introduce some of the more bizarre characteristics of the post-holocaust Metro, such as shadowy ghosts of deceased humans and even events that are forced to replay their last moments forever. Haunting voices of laughing children are audible from the pipes installed in the walls of the tunnels, and glowing globes of electricity called Anomalies travel the tunnels killing anything in their path. The journey leads both men to a war-torn Cursed Station, where Artyom is tasked to retrieve explosives from the tunnels and detonated them in different places to block waves of mutants that endanger the station.
In success, Artyom part ways with Khan and shortly after reaches Armory Station, one of the many station controlled by a Soviet Communist-like group. He stumbles in on an interrogation and is almost arrested, but manages to escape with the help of a stranger that is killed in the attempt. Artyom hides with a man named Andrew 'the Blacksmith' under a trolley tasked with carrying troops to the border of the Communist controlled part of the Metro, where a war against Neo-Nazi survivors rages on. Here, Artyom must fight his way through the front lines, through both Nazi and Communist soldiers. After fighting his way through, he is captured by the Nazis. The Nazis prepare to execute Artyom, but before they can, Ulman and Pavel, two more Rangers appear. Ulman kills the Nazis with a knife. Artyom presents Hunter's token and Ulman tells Pavel to take Artyom to Polis, and to meet up with him later.
Pavel and Artyom steal an armored mine car, and attempt to pass through the Nazi barricades while posing as Nazis. They are discovered however, and are chased down the Metro tunnels by more armored mine cars and a tank-like train. After making it through the Nazi barrier, the two proceed further into another smaller mine car, but are ambushed again by Nazi troops and forced to flee, by chance reaching a massive underground depot for trains. Upon reaching the depot, the car is attacked by hordes of mutants, Pavel is killed, and Artyom barely makes it out alive. He reaches another settlement, Hole Station, where he is hastily recruited to aid the defenders in fending off a massive attack of mutant creatures. The defense fails. Having received a distress signal from the leader of the defenders, who was heavily wounded in the assault, Artyom is tasked in transmitting it to Polis before reaching it, and has to traverse the now ruined station, filled with mutants. There, he meets a young boy named Sasha, who survived the massacre, and carries him to safety, meeting the other survivors shortly thereafter.
From there, Artyom makes another trip to the surface, this time through Nazi-controlled territory, stopping briefly to transmit the distress call from Hole Station. He journeys through another station, Black Station, where he meets Ulman at the end. After fighting their way through more Nazis, the two ride away in a trolley and finally reach the heavily fortified borders of Polis.
In Polis, Artyom presents the token from Hunter to Miller, and the two explain the threat to the ruling council of the station, asking for help. However, the council dismisses the threat because of lack of resources and men that are needed for eventual war against the Nazis, and because they underestimate Artyom as a superstitious guy from some remote station. Hope is renewed when Miller pledges his assistance to stop the Dark Ones and save Exhibition, along with the rest of the Metro. He proposes that a mostly intact military launch facility, known as D6 can be used to eradicate the Dark Ones with "the same fire that gave birth to their kind." The location of D6 was lost at the onset nuclear war, so the Rangers are forced to travel again to the surface and reach the Russian State Library, whose military archives hold documentation of D6's location.
Miller, Artyom, and Danila (another Ranger) set out for the Library. On the way, Danila is injured and taken back to Polis by Miller, leaving Artyom on his own to find the documents. As Artyom moves through the library, he encounters horrific ape-like mutants called 'Librarians,' quasi-intelligent creatures that were once human. He is forced to battle through many of these beasts, the sole inhabitants of the Library, but he succeeds in retrieving the documents. When Artyom leaves The Library, he is confronted by a Librarian. But before the Librarian can attack Artyom, Miller and another Ranger, Stepan, run it over in an armored car. They take Artyom to Sparta, an above-ground Ranger outpost, where Artyom meets the remainder of The Rangers: Boris, Vladimir, and several unnamed characters. He also meets Khan again, who with cryptic speech hints at the fact that the conclusion of his journey, be it bloody or not, rests only in his hands.
From here, the group of Rangers head to D6. Boris and Stepan are killed fighting their way through hordes of mutants. After reaching D6, a massive military underground bunker, the remaining Rangers search for the missile command center. They find it, but it lacks power. This forces Artyom and Miller to reactivate the facility's reactor manually, forcing them to battle their way through strange amoeba-like entities, possibly the mutated results of biological weaponry. As they complete their task and ascend again, they discover that the base still houses large amounts of military hardware. Miller marvels at the arsenal; it renews his hope of conquering the surface once again.
It is here that the game's prologue turns out to be its epilogue. As the sole survivors of the mutants' assault, Miller and Artyom fight their way to Ostankino Tower, carrying a laser pointer to direct the missile salvo from D6. However, it must be placed on top of the tower to be effective. During the ascent, Miller is injured by a flying mutant, and Artyom must complete the journey alone. Arriving at the top and planting the beacon, he is forced into a powerful hallucination by the Dark Ones. He travels through a bizarre landscape, at the end of which he encounters Hunter's ghost. Escaping the hallucination by defeating a looming Dark One, Artyom's journey ends.
The game has two possible endings. Different points of the game calls for the player to make certain choices, for example whether or not to help a beggar by giving him a bullet or to use stealth instead of aggression to bypass a level. If the player does not make enough of such choices (which in-game are notable for brief flashes of light), then the game ends with made enough good choices, then he can destroy the pointing device and save the Dark Ones. It is then revealed that they were not approaching humans to attack them, but to communicate with them, and that they wished for peace between the two species.
There are notable differences in the ending monologues spoken by Artyom and the Dark Ones. In the events of the normal ending, the Dark Ones perceive Artyom as a threat, and after succeeding in activating the device, he is left with doubt. If the Dark Ones are spared, it is then revealed that they were not approaching humans to attack them, but to communicate with them, and that they wished for peace between the two species.
(Wikipedia)