What if The Enterprise found a bunch Aliens/Xenomorphs on a ship?
That might have been very funny but also tragic as hell, turn those Aliens/Xenomorphs from the Alien movies into a minor nuisance by having The enterprise find a ship adrift in space with minor life signs, they are coming from the dead bodies on the ship in question.
A scan while onboard reveals parasitic alien creatures inside, Chestbursters, dead Facehuggers are on the floors of the ship, maybe a member of Worf's security team would get bitten by a Chestburster or a Facehugger, they go to sickbay and scare the hell out of Dr. Crusher when she sees the creature growing inside of them or heaven forbid if it emerges from inside of them while they are inside sickbay.
Not enough of a threat to take down the ship, but enough of a threat to kill some minor junior officers and give Worf something new to kill, maybe even Worf could fall victim to a Facehugger Alien/Xenomorph and require urgent care to avoid death.
Would make for a fun and gruesome crossover with Aliens and Star trek, especially if Barclay or Worf got into danger, Data being grabbed by a Facehugger would just be funny, Troi would just be sad.
On another note you could make it into a accident involving the Pakleds for example, raiding a ship to steal their technology and stuff, only to encounter the Aliens/Xenomorphs creature, then The Enterprise comes along later and encounters the bloody aftermath of it all.