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They are the remnants of survivors of the nuclear holocaust who have mutated into a new species. The dark ones posses psychic powers and are encountered by Artyom numerous times throughout his journey. In the world of Metro 2033, there is a great deal of speculation as to the nature of the dark ones, with some believing that they are the next step in human evolution or a distinct sub species.
Dark ones can control other mutants telepathically, though have trouble doing so with sentient creatures such as humans. In addition they are resistant to cold temperatures and radiation, most likely due to evolving in the post apocalypse. While they appear to be the games antagonist, attacking the player on multiple occasions, these "attacks" have actually been attempts to communicate with Artyom who they have chosen as something of an ambassador for the human race due to his resistance to their telepathy. Previous attempts by the dark ones to communicate with other humans had caused them to accidentally kill them because of the nature of their telepathy, and so they choose to communicate with Artyom.
In the end the player can choose to murder a dark one at the top of the radio tower and launch a missile barrage against their home, Kievskaya station ( where the dark ones evolved from humans ), and this is considered the bad ending. Alternatively Artyom can halt the missiles and save the dark ones, realizing their nature and that they had been helping Artyom all along. As of Metro:Last Light the bad ending is considered the canon ending.