What I would really love to do with this game is mod this into a horror game. I know, what???
If you go back to TOS, there were horror scenarios in that series with monsters in mines, colonists dying for unknown reasons, salt-monsters, lava-monsters, and all sorts of creepy-crawly monsters and alien life forms shambling about. The scanners (ship and hand) could not always tell us everything, we had to crawl around in caves and mine shafts, and stay in colonies and have the woman's scream in the next room. Even the transporters did not solve every problem.
By the time we got to The Next Generation we mostly forget about horror. The "unknown" became really theoretical and we were modulating shields and phase capacitors to solve "big science" problems (but always with a personal cost, so it wasn't so theoretical it did not have an impact). And if I did a horror mod to this game, it would be in the TNG era.
I just like the concept of taking a society that thinks it knows everything, has perfect scanners and a science established that can play with space and time, a theory and conceptual framework for everything, and knocking it down a few rungs of the ladder.
You Don't Know Everything
Don't be so sure of that "science" of yours.
The results of scans? Likely wrong as the evil "Hellraiser force" manipulates the results to get you to send crewmembers to their deaths. Transporters? They can be unreliable and whatever this evil force is controlling the galaxy can transport your away team into a hellish trap, chained up on a wall, into a deathtrap, or never to be seen from again. Weapons? Not always effective against the things which lurk about.
Yes, I know, crews would be playing it safe by taking the shuttle most of the time. But there is a risk and a cost to using technology. Even a scan by the ship's sensors could get this "feedback loop" and cause the science console to explode with an overload, and possibly kill the crewmember doing the scan. You have to be prepared for the worst, and every decision to use technology should have a chance for a terrible cost (perhaps on a critical failure roll death is certain, no matter what you are doing).
Your starship? Not always a safe place as the hallway lights blink on and off as the force probes and searches for life to torment, things escape from the lab, crewmembers mutate into bloodthirsty monsters, and accidents do happen. Some of your crew let their baser desires control their minds and turn evil on you. Perhaps one wakes up with totally black eyes and tries to kill everyone. Strange mutations happen in crewmembers and are not always understood, and perhaps they are benign, or perhaps they will drive the crewmember mad. Maybe the crewmember will grow into a room-sized monster. Maybe they will grow devil-like horns and be fine. Or perhaps, "fine." And other members of the crew whisper about this "freak" and mistrust spreads.
Every thing you were certain of becomes an unknown.
You can't trust your ship, science, technology, weapons, or even your crew.
Just Add Alien
Free League's Alien RPG has a lot of great tables for stress, injures, panic, and wounds I may wish to borrow from. I love the concept of an ever-increasing stress pool that leads to panic. I would not do Xenomorphs, but the rules for a lot of the conceptual fear and horror mechanics (if I choose to use fear mechanics), would fit right in here perfectly.
The Dark Universe
This would be a parallel universe sort of experiment, sort of The Dark Universe sort of thing where TNG at the end of the run splinters off into a universe which becomes overrun by evil power, the Federation begins to shrink and decline as planets fall into madness, and the over-arcing meta-plot is to solve problems here and there to keep the ever-encroaching madness and insanity at bay.
There would be "safer" hub worlds where things felt normal, but the edges of the frontier would be lost to madness. There may be sadistic raider ships flying about in a Mad-Max style of orgy of violence and piracy out there, so there would be a few fun "straight combat" options for missions and breaks in the horror. A lot of the missions would be going to a colony world to solve a problem that would force the world more into the darkness, like miners uncovering a strange idol that causes madness, creatures on a space station, or other classic monster and horror-style adventures.
Since you can't always be under threat, the hub worlds would be relatively safe, and provide that needed contrast between "the normal world" and the terrors of the periphery. If everything is horror, then there is no tension. There needs to be safe harbors and normal life.
And then you are sent out into the darkness.
If you succeed (often at great cost), that remote colony is safe for a while. The threat level goes down. And your ship is sent to the next flashpoint where the evil tries to dig its claws into the innocent minds of the world. The cost would be high as your ship would be constantly losing crew and having them replaced, and perhaps your ship itself would be lost in the fight, but to serve in this Federation is to defend the peaceful worlds from this cosmic horror, at any cost.
Perhaps you survive long enough to make it home.
Perhaps you earn the chance to retire and your mind cannot take it anymore.
Perhaps you are chosen to train the next recruits for their first mission into the darkness.
It is a fatalistic and noble game where the ship and its crew know they are fighting a losing battle against the impossible, with their very lives and sanity at risk, but to win another battle against evil and push the madness back a few parsecs makes every sacrifice mean something.
Or perhaps not. This is horror, after all.