FreeSpace 2 has this incredible build-up about the nature of the alien threat, starting out as just a secondary antagonist, and then increasing and increasing in threat, until you as the player come face to face with the reality of an unstoppable apocalyptic threat that you can only ever really run away from. I think it works so well because the game really is a power fantasy for most of it's run, with the player regularly overcoming seemingly impossible odds (the solo bombing run against the gargantuan Sathanas juggernaut is a standout)... but the ending levels just have the wheels coming off the bus, and the climax comes whether you survive it or not. Pretty good for a wing commander clone.