- To start, there's "Home", one of the most infamous episodes of the whole show, and the only one that was never shown on Fox again for several years after its premiere (it can now be seen on DVD and Netflix streaming). A Mundanger that starts with an inbred family burying a hideously deformed baby outside their farmhouse and gets worse from then on, it's an episode that would likely push an R-rating as a film. The rest of the story features moments like a family being beaten to death with baseball bats, impromptu death traps, and the reveal that the Peacock family sons keep their limbless mother under the bed and try to impregnate her—in fact, the eldest brother is the father of the other two, and all three are the father of the dead baby. How it got past the censors with just a viewer discretion warning is still a mystery worthy of a Mulder and Scully investigation.
- In the second season episode "Blood", Mulder is sprayed with an experimental chemical that is shown to cause subliminal effects to its target and sees an attractive woman on TV advertising a fitness center. The words on her shirt? "DO IT."
- In second season episode "Aubrey":
Mulder: Well, I'd like to know why this police woman would suddenly drive her car into a field the size of Rhode Island and for no rhyme or reason, dig up the bones of a man who's been missing for 50 years. I mean unless there was a neon sign saying 'Dig Here'.Scully: I guess that's why we're going to Aubrey.Mulder: Yes, and also, I've always been intrigued by women named BJ.
- Deep Throat. Of course, the name is a reference to Woodward and Bernstein's famous informant, but it's pretty incredible that they were able to say that phrase — on network television — so many times given the porn film and sexual act that it really referred to.
- In the 7th season episode "Signs and Wonders," the agents investigate a church that practices snake-handling. Scully says snake handling is something she never learned in Sunday school, and Mulder replies, more crassly than usual, "funny, I knew Catholic schoolgirls who were experts at it." If that went over your head, he's referring to handjobs.
Radar / The X-Files
The truth is out there... but so are sexual innuendos, dark and horrifying moments, and Squick that could push the boundaries of network TV.