There's an Open Letter to DOOM fans on HomeLAN Fed where scriptwriter explains the changes to the DOOM story for the film adaptation, responding to concerns that what story the game originally presented is being changed:

The screenplay I wrote DOES differ in a number of ways from the games. I want to be very honest and forthcoming in saying that, and I know that I won't make any friends amongst the fans of the game in doing so. But it should be mentioned that it was never the goal of anyone involved in this film, from myself and the producers to the studio to the guys at id, to make a direct film adaptation of the game(s). The thought process has always been to create an extension of the Doom universe that will give fans an interesting new take on the themes that they've come to enjoy in the game. Because let's be honest here: as far as a completely immersive and cinematic experience, we were never going to top Doom 3 anyway, and we all knew that. Instead, we have toyed with some elements of the game, and yes, I am pretty much solely responsible for that, since it was my pitch and my screenplay that got made. Let me assure you, though, that the themes and elements that you love about Doom are ALL represented strongly in the film...just with some new twists.