The story has always been my favorite part of the original Marathon. That, and the environment, ambiance, and orientation/wayfinding parts of it And as I've gotten older, I've liked the guns part less and less. I would love it someday if somebody could make a different type of game in the marathon story universe.
Like an urban explorer game where you are looking for a switch to open a door, but you might run into an alien S'pht compiler around the corner.