When an air force pilot goes missing last seen covered in an unknown rash, Mulder and Scully must travel to an air base which is nicknamed Area 51.

Mulder continues to investigate this case despite the warnings the of a certain mysterious character named Deep Throat (after the infamous watergate informant) in a Washington bathroom. He warns that the government are dangerous and will even kill to stop the lone truth seekers finding out the truth, like Mulder.

When the missing pilot returns, everything seems okay just for two things, his wife thinks he is an imposter and when questioned he couldn't even remember how to fly a plane! So Mulder is led by two teenagers to the remote air base to look for evidence and is quickly tracked down and injected with a substance that erases his memory of the previous events.

The agents travel back to see the pilot's wife and find her to be quite uncooperative, obviously having been threatened by the government. It goes to show that everyone is out to stop you