I just wanted my wife to make me soup...
Four months later, Mulder tells Scully that Budahas hasn't been seen since his arrest, and six other pilots have vanished the same way. When he goes to the bathroom, an informant appears (seemingly out of nowhere-Apparition is also a thing), and warns him away from the case, and that Mulder is being watched.
Naturally, this means that our heroes have to visit Idaho. Mrs. Budahas says the colonel had been behaving strangely, as did another test pilot nearby. Scully tries to make an appointment with the base's director, but is consistently put off. A local reporter, Paul, has been looking into the strangeness as well, and directs the two to the local bar where UFO groupies hang out, and, presumably, talk about that time they totally followed Ziggy Stardust on tour, for realz you guys. The bartender tells them to watch the base from an adjacent field.
Once there, they witness strange lights, and then are chased away by a black helicopter, running into a teenage couple while they're at it.
When Scully and Mulder return home, they find out that Colonel Budahas has come back home. His behavior is fairly normal, except for one thing: he has no memory of ever flying a plane or helicopter. They are stopped on the way back by men in black (no, not Will Smith), who take all their papers and order them to go back to D.C.
Mulder does what Mulder does best. The teenagers show him how to get onto the base via a field (afterward fretting that they didn't warn him about the landmines). On the base, he witnesses a saucer rise up from the ground. However, he is caught and taken to a lab.
Fact: aliens' main attack is bright lights. This would eventually translate into the dreaded Lens Flare.
Scully wakes up the next morning to find Mulder still isn't back, and all the phones in town aren't working. While talking with Paul, she hears orders being given to him over a walkie-talkie, and realizes he works for the base.
Then Scully explodes into awesomeness. She forces Paul. at gunpoint, to take her to the air force base. Mulder is brought out, with no recall of what happened or what he saw.
Scully's report is ignored by her superiors. While Mulder is out jogging, he runs into "Deep Throat" again. Chillingly, the man tells him, "They have been here for a long, long time."
Exhibit A: Giorgio's hair.
This took a common theme among the UFO and alien theories, the government reverse engineering from alien technology, and ran with it. It also showed us a lot about both Mulder and Scully. Both are willing to take great risks, both for the truth and to protect each other.