It is going to be a first person science fiction/ horror on which I focus on the idea of hostile alien and human interaction. The game is not going to be a shooter or strategy, but focus on the themes of fear and hopelessness when faced with unbeatable odds.
My most memorable sci-fi horror game was System Shock 2, and whilst it was a shooter, there wasn't actually that much shooting in it, as both ammo and health were kept very scarce and you were constantly forced to go and search for it, whilst all the time knowing that the very last thing that you wanted to do was to go exploring away from the main path, because by doing so you placed yourself in extreme jeopardy. This push / pull dynamic is very unsettling on the player. Countless games have used it to great effect, Metro, Stalker, L4D, HL, etc, but for it to work well, you have to get the push / pull balance right. In your shoes I would certainly have a think about how I could build this dynamic into my game.
One of the other things that SS2 did was to tell both the background to the events in the story, and part of the story itself, by finding and listening to the audio logs of dead crew members and to use them to build tension. For example, I remember finding an audio log in a blood splattered room, and listening to the victim narrating/recording their last moments, which die away to screams and the noise of the bad things that killed him/her. The sting in the tail though was when you suddenly realised that those same bad noises are coming from both the audio log recording in your hands, and from outside of the room that you are in currently sitting in. Yes, it's a Mines of Moria / Tomb of Balin trick that many games, authors and film directors have used before, but the sheer tension and terror that good audio can create, with no actual bad guy in sight, is amazing. For me, the best example of audio used to create tension and terror in a video game is probably the Cradle episode in Thief 3. However, as you are going sci-fi, and alien, then you need to think long and hard about the how the aliens sound, even if the aliens are completely mute. Think Jaws. That menacing theme music isn't what a shark sounds like, but play it to half the planet, and they will instantly think Shark. Likewise concentrate on the atmosphere. The noise of the rain in Blade Runner, the wind in the Thing, etc. As for how the aliens themselves sound, go find something in nature and distort it, as it will sound a million times better than anything you could artificially synthesize.
Shock, horror and fear are all a lot easier to replicate in a game, than is hopelessness. In fact I would steer well clear of hopelessness all together, other than for plot crucial moments. For the player to truly immerse themselves in the game, they must have and be able to maintain hope. That means setting up situations where they can succeed in different ways, and again I would refer you to SS2. There were loads of little puzzles spread throughout the game, and even if you were making a complete mess the overall meta game in terms of discovering and conserving, ammo, weapons, health, augments, etc, you could still limp along buoyed up by the success of solving the puzzles and the progression to new levels. You always had the sneaky suspicion that you weren't doing as well as you should have been doing, and it was a bit like a game of Civ. Civ is actually a good example of a game that does produce genuinely hopeless situations, that the player simply can not win, should they mess up big time. However, the critical "reveal" doesn't happen until they have settled loads of cities, discovered loads of tech, built wonders, improvements, units, met the other civs, etc. In other words they had a lot of fun trying and often succeeding at the tactical side, (hope), but are then kicked in the teeth on the strategic side, (hopelessness), and so ultimately lose.
As for specific story ideas and inspiration, well I would steer well clear of open air alien worlds unless you have an impressive amount of imagination. Linear spaceships, orbital structures, alien laboratories, etc, would be the easy route to go, if you have limited resources / budget, etc.
The simplistic stuff works the best, and you only have to look at HG Wells to see that. War of the Worlds placed humanity in as hopeless a situation as they could be. The culture gap was so great that the aliens didn't deign to interact at any point with humanity, other than to kill or harvest them. The technology gap was so great, that they had won. Humanity was being exterminated, our biosphere was being changed, and our species was on the brink of extinction. Alien means other, and War of the Worlds do "other" brilliantly. No explanation, other than colonisation, and humanity utterly powerless to prevent it. In fact I would go a step further, as it's often better not to explain why the aliens are doing what they are doing.
So, sticking with the theme of keeping it simple, how about an interesting idea that's never been done before in games, namely the = "Jinn"? No, I'm not talking about the friendly Disney version, (which has obviously already been done), but about the sinister and intriguing historical version. Go look them up, and you will see what I mean, as the hostile / hopeless interaction is already built into many of the myths.There are a thousand different ways you could spin that story, but as you want Aliens, then just make them from another dimension or planet, and the myths surrounding them give you the ready made back story that they have been around for thousands of years. Given that their science and technologically would therefore be beyond our comprehension, you don't actually have to explain much about their intentions, purposes, etc, unless you particularly wanted to. In your shoes, I would probably float a few ideas regarding why they are area specific to that region, and why they are here, why they have been here so long, what they are doing, etc, but much like the myths, I would leave it unexplained, and as conjecture only. It really depends on which of the various origin myths tickles your fancy, (there are a surprising number of them), but it would be easy peasy to spin out any number of different and fascinating sci-fi stories based upon any of them. Drop some learned quotes into the game, such as architectural, religious and historic references, and teach your audience a few things regarding the "Jinn" to get them thinking, because most of your audience won't know that the sinister version even exists, or that it has been around for thousands of years. As for the game, and the story within the game, well the only limit to that, is your imagination.
Regards - Mr P