Ambience is definitely big. For your idea specifically, it would be important to hint to the player of what happened, i.e. have him/her come across bodies, rooms that have been trashed, places where it was obvious a last stand took place (like in the movie Aliens). Make it quite apparent where things are going, so that the player builds up anxiety. If there is no tension before a startling moment, then the moment isn't all that startling, and the initial shock wears off. It's all about context. What wouldn't be scary in one map, might be totally freaky in another because of the story line and the setting. Good luck, dude.