According to the Doom Manual, Phobos is used to store nuclear waste, and is also the home of Teleportation experimentation with Deimos. Sometime before the game however, an experiment goes wrong, Deimos disappears from sight, the Phobos base is attacked by an unknown force, and the player's squad is sent up to investigate. The squad ends up being defeated sometime later, and the Lone Survivor ventures into the base, eventually defeating the Bruiser Brothers and supposedly dying after being teleported.
In Doom 64 the Phobos base is sealed, and bombarded with "apocalyptic amounts of radiation" which allows the Mother Demon in a crippled state to resurrect the dead demons, a nearby satellite detects this and in a dying message relays this back to Earth, and the Doom Marine is sent back to Phobos to defeat the demons.
In Doom (2016) Phobos (and Deimos) are used as mining stations, although it is never stated, or implied that any outbreaks, or military operations occurred there.
Behind the scenes
In Doom, Phobos is depicted with Earth-like gravity, a thick atmosphere, and tall, seemingly vegetation-covered mountains; the sky texture for the episode was derived from a photograph  taken of Yangshuo Cavern in China.
In reality, Phobos is a asteroid, some 20 kilometers in diameter with gravity less than a thousandth of that on Earth, and no atmosphere (even if an atmosphere could be generated artificially, the moon's gravity would be insufficient to hold it in place without its own artificial gravity). To be more plausible, future releases (Doom 3, and the 2016 reboot) moved the plot to Mars.
- Phobos on Wikipedia
- Phobos (character)
- Phobos Labs (Mars)
- Bazoik (has an analogous story in Chex Quest)