Star Trek: 10 Alien Encounters Before First Contact
6. The Xindi - Carpenter Street
While this episode almost caused actor Jeffrey Dean Morgan to switch professions, it serves as one of the grim examples of how alien encounters are not always pleasant - and we're not even going to mention those Borg that travelled back in time either!
The Xindi Reptilian faction had been, with a little help from the Sphere Builders, experimenting with biological weapons. For this to truly work, they needed human subjects to test, so a little time travel was called for. Leland Orser, returning to Star Trek, appeared as Loomis.
This blood bank worker has been kidnapping people for use by the Xindi, even if he wasn't initially aware of their alien origin. Surely, somewhere along the way, he must have questioned - but still, he's a kidnapper-for-hire, though finally is forced out of work by the intervention of Archer and T'Pol (who still may or may not accept that time travel is possible).
While Loomis is thankfully arrested for his actions, and the Xindi Reptilians are brought back to the future, this alien encounter would certainly fit the bill as one of the more dangerous run-ins with extra-terrestrials.