ALIENS IN "PAPER CLIP"

Frank,
I've been rewatching my "X-Files" DVDs and most recently saw "Paper Clip", which is my all-time favorite episode. To this day, I have no idea what's happening when Mulder and Scully are in the mountain cave in West Virginia -- the one with the files of individuals born since 1950.
Why was a UFO seemingly there, and more importantly, why were a number of aliens running past Scully in the cave? I've never understood this and would love to solve this long-running mystery of mine.
Thanks,
Brent
Cleveland

I'm so glad to hear that -- I share your enthusiasm for that episode, so I hope you won't be frustrated by my answer. You're not meant to know what the aliens are doing there. At that point in the series, all we wanted to establish was that the aliens were, in fact, connected to the Strughold Mining Company. (And Scully wasn't even meant to be certain of that much.)
I wouldn't attempt to fill in the details about what they were doing there, any more than an artist should tell you what's in the dark shadows of a landscape painting. You're not meant to see into those shadows -- you're meant to imagine and fill in the blanks yourself. Having said that, if you follow the mythology through subsequent episodes (and particularly the first movie), it's not hard to surmise what the little grey guys might have been up to.