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Doom: Knee-Deep in the Dead is the first in a series of four officially licensed tie-in novels to the original Doom series of games in the mid-1990s. All four volumes were reissued in 2005 with new cover art.
This book follows the storyline of the first game fairly closely, although the origin of the monsters is changed from Hell to a mysterious alien civilization. Ever since its publication, some Doom fans have referred to the in-game protagonist as "Flynn Taggart", even though that character was intentionally not given an official name  .
The prologue opens in the Middle Eastern country of Kefiristan. Fox Company leader Lt. Weems orders his men to open fire on civilians. Cpl. Flynn "Fly" Taggart, the narrator, attacks him.
Before Fly can be sent for court-martial, however, Fox Company is called to the UAC research facility on Phobos to deal with a disturbance. Fly is kept under guard while the other Marines are sent off. This turns out to be Fly's saving grace, however, as the rest of Fox Company is wiped out by the invading forces. Escaping, Fly encounters several zombies, followed by a run-in with an Imp.
Moving deeper into the complex, Fly finds more monsters, as well as "A.S." arrow marks on the walls; PFC Arlene Sanders, his friend, has apparently survived. Ultimately, Fly reaches the two Barons, defeats them, and is transported to Deimos Base, completely naked. On Deimos, he locates Arlene and regains clothes and weapons. The two eventually track down the Cyberdemon and defeat it. Teleported again, Fly and Arlene arrive inside a gigantic fleshy enclosure, and field-strip corpses for clothes and weapons once more.
Here they meet Bill Ritch, a UAC computer programmer whom the Spider Mastermind captured and tried to interrogate. The three make their way through this complex, ultimately defeating the Spider Mastermind at the cost of Ritch's life.
Returning to the surface, they find they are still on Deimos, which has been moved into Earth orbit. The giant dome that holds in their oxygen has cracked. Worse, they can see explosions all over Earth's surface — the invasion has already arrived.
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