Did you not watch any episodes? The aliens and conspirators conducted their experiments on abductees, in addition to Scully and Duane Barry, in order to create alien-Human hybrids to serve the aliens as a slave race. The aliens didn't utilize any form of anesthetic because they tried to subjugate other alien cultures in order to conquer the universe.

Right, I knew that. It just seems kind of unfair.

You're right. But the aliens and conspirators were evil. What did you expect?