I got two words for ya’…
“Ghost Ship” (or “Flying Dutchman”, if you wheel)…
Player’s, all comfy inside their ship after ‘another successful mission’, when ‘it’ happens: sensors detect the form of a ship floating derelict in space (a transport, a cargo hauler, a scout…). Upon further exterior scans, it discovered that this ship (listed to the Federation/Starfleeet) has been ‘MIA’ for quite some time (60-100 years, but your mileage may vary). Starfleet Command would insist upon an investigation as to what happened.
The ship is coated with particles that refract and deflect the scans to the interior, and transporters can’t penetrate, so a shuttle must be used. Once over there, the crew of the shuttle discover that the ship has little life-support (no heat, thin atmosphere, lighting that's hit-and-miss...mostly miss), so on go the e-suits (making them ‘a little slower’ in the reaction department). Armament wise, the best the players could get ‘for this mission’ are type-II phasers, and each character has a tricorder (mostly the ‘generic’ ones, with a few ‘specific’ one: Engineering, Tactical/Security, Medical,…).
While over there, the crew discover that the ship’s crew were attacked and killed by something that they brought aboard…that’s been in hibernation on ship since the last of that ship’s crew was killed/died…until the shuttle’s docking woke it up.
The ‘creature’ could be anything: A new breed of Jem H'adar warrior, a eugenics soldier, a borg, a…well, you get the idea.
In any case, the ‘creature’ seems impervious to phaser fire (via armor, shields, phasing, or any combination of them). Oh, and have a few ‘Ensign Jimmy’s on hand to hand demonstrate the ‘creature’s’ powers, abilities, and just ‘mean spiritedness’.
The best two sci-fi example of this idea are ‘The Thing’ and the DS9 episode ‘Empok Nor’, the latter especially ‘Trek-wise’.
...and that's about the time it hit the fan...
Truisms I know:
1) Marvel is NOT better than DC (nor should EVERYTHING be ‘ULTIMITED’),
2) D20 is NOT the best gaming system out there (nor should EVERYTHING be ‘crammed’ into it),
3) And No matter how ‘THEY’ dress it up, Regardless of how ‘THEY’ title it, and even if ‘THEY’ say “BASED ON…”; “ENTERPRISE” IS NOT STAR TREK!!!
4) 'Reality' T.V. ain't 'Real'