26. "Paper Clip"
The concluding episode of the mythology arc begun at the end of Season 2 sees Mulder and Scully discovering an underground filing system where the government keeps a catalog of everyone vaccinated against smallpox. Also, Mulder encounters the suave, new antagonist Well-Manicured Man (John Neville), and Assistant Director Skinner tells the Cigarette Smoking Man to "pucker up and kiss my ass." Just amazing.
A gorgeously meditative standalone, this episode follows Scully to New York City where a photographer cursed with immortality attempts to photograph the Grim Reaper so he can finally die. Geoffrey Lewis is is wonderful as the weary shutterbug and he makes for a terrific sparring partner with Scully as they discuss at great length whether anyone can truly have too much life.
24. "Deep Throat"
The series' second episode sees Mulder and Scully investigating the disappearance and reappearance of several military pilots, and also introduces the mysterious character Deep Throat, who acts as Mulder's informant for much of the first season. This sets the template for the mythology episodes to follow, and features a killer final scene in which Deep Throat casually suggests that aliens have been here "for a long, long time."
The conclusion to the story begun in "Sein und Zeit" sees Mulder finally gaining clarity on his sister Samantha's disappearance, thanks to a psychic detective played by Anthony Heald. A deeply moving installment, especially notable for how it reveals the full, demonic scope of the Cigarette Smoking Man's motivations.
A legless Indian beggar, brilliantly played by Deep Roy, is able to literally crawl inside fat-cat Americans and devour them from the inside. After he insinuates himself into a small American town, Scully and Doggett come calling. A provocative standalone that deals with Western-shaped prejudices, and also fascinatingly explores Scully's ingrained inability to make Mulder-like leaps of logic.
21. "Bad Blood"
Mulder and Scully have conflicting viewpoints on the case of a pizza delivery boy (and maybe-vampire) who ended up dead on their watch. Sheer hilarity, this Vince Gilligan-penned standalone features a bucktoothed guest turn from Luke Wilson and a stunned Mulder singing the theme from "Shaft."
20. "Small Potatoes"
Five West Virginia babies have been born with tails, and Mulder and Scully determine the culprit is the lowly janitor Eddie Van Blundht (Darin Morgan), an unexceptional man except for the fact that he can shapeshift. Another comic gem, this episode hits a high when Van Blundht disguises himself as Mulder and attempts to woo Scully.
A creepily captivating John Hawkes plays Mulder's neighbor, Philip Padgett, an author whose words are murderously alive. When he becomes romantically attracted to Scully, he attempts to write her into loving him. A very meta and wonderfully macabre episode.
18. "Sunshine Days"
Vince Gilligan wrote and directed the series' last standalone episode in which an antisocial man (played by Lost's Michael Emerson) psychically recreates his home as an exact replica of the Brady Bunch house. It's a humorous and moving testament to Gilligan's time on The X-Files and a nice sendoff for the Doggett and Reyes characters, who take more of a backseat in the series finale.