Trent Reznor has spoken on the official NIN website about Doom 3, the reasons why his work did not make it into the game and on his relationship with John Carmack.
According to Trent Reznor, the initial plans for Doom 3 called for no musical soundtrack as such, but a musical, immersive environment. A theme tune to accompany the game intro was planned but according to Mr. Reznor, ...time and money and bad management... did not let the collaboration work out.
The initial plans for the involvement of the NIN lead singer called for total control over the game's audio, as an overall sound producer, ...from foley and voice over to ambient world noise.. Work on the audio involved working directly in the game editor and with the programmers. Trent Reznor describes his work, during that time, at iD as ...thinking in a different way... The overall effort focused on bringing the environment to musical life by ..."tuning" various environmental sources so they 'd cohesively interact with one another in a "musical" way. Imagine your footsteps, as part of an orchestra which may also include a nearby dripping ceiling and the creaking of a door.
The NIN front man still claims to be eagerly awaiting Doom 3 and to be looking forward to trying out the powerful new engine. You can find a link to the full Trent Reznor interview by following the download tab above.