There must be a scene where Mulder tracks down Cameron Mitchell after he gets shot down but before he joins the Stargate program. Mitchell, wheelchair bound due to his injury, drinking heavily, and on Morphin, confesses the whole truth to Mulder. " I was shot down in Antarctica while defending earth from an alien invasion by a fleet of ships. I was leading a squadron flying a secret fighter jet built with reverse engineered tech from crashed alien spacecraft. We only won because a general in the USAF got control of an abandoned weapons platform built by other extinct aliens."

Cut to Mulder and Scully leaving the apartment building "And you think I'm crazy. This guy fell down the weekly world news rabbit hole and hit his head on every rock on the way down." Mulder says.

"I didn't see any of those magazines in his apartment Mulder. He's a decorated colonel in the air force."

"The best of us know to hide the stacks of UFO magazines when we have company." Mulder quips.