Mr. Mulder, They have been here for a long, long time

 One of my favorite first season episodes remains Deep Throat. Not just because Hardin's insider who knows a lot and seems capable of guiding Mulder towards truth...but in a certain way, done in a calculated approach. Sometimes Mulder can be too stubborn to listen to advice. Like when he's told not to go to a secret airport base in Idaho, not located on any reputable map. Could Roswell alien aircraft wreckage have been shipped to this base and years later that technology lead to experimental stealth planes capable of incredible feats? Mulder is willing to take a chance, using the disappearance of a pilot who might just have been in the cockpit of such stealth aircraft as a means to get to the precious truth he always pursued.