In late 2013, a nuclear war occurred. Russia was targeted with atomic bombs, causing severe radiation across Moscow, forcing the rest of the people to live underground in the metro stations away from the deadly effects of radiation. Many animals and humans left behind mutated into creatures known as the Dark Ones, who were left outside for the next 20 years.

In 2033, Artyom (Russian: Артём), a 20-year-old male survivor and one of the first-born in the metro, learns from an elite soldier and mutant hunter, or Ranger, named Hunter that a group of mysterious creatures referred to as the Dark Ones are threatening his station in the Metro. Hunter gives Artyom his dog tags and tells him if he does not come back, he must go to Polis and present these to see if they will help his station.

Artyom must travel through territory occupied by Soviets and a Fourth Reich, and infested with mutants as well as the much changed surface of Moscow. Once in Polis, he meets with a Ranger named Miller, who agrees to help him. Miller knows of a missile silo known as D6 that has the firepower necessary to destroy the Dark Ones. Artyom, Miller, and several other Rangers reactivate the command center for the missiles, and Artyom installs a laser guidance system on a nearby radio tower. After the laser system is installed, Artyom experiences a vivid hallucination induced by the Dark Ones.

After the hallucination, two endings are possible, depending on choices the player makes throughout the game. In the normal ending, Artyom allows the missiles to fire, destroying the Dark Ones. The alternate ending gives Artyom the choice to destroy the laser guidance device, citing a last-minute realization that the Dark Ones were actually attempting to make peaceful contact through the hallucinations.