I do realize I’m cheating a bit as I am including multiple continuation episodes as one
I’m struck by how different this list is than what it would have been five or ten years ago. Here are my reasons.
The Unnatural written by David Duchovny has grown on me as I become more aware of David Duchovny’s other written works and of the unique style he has of lightness and dark. Unnatural is such a perfect example of this as a fairy tale with a baseball themed storyline and a backdrop of racial segregation and the Ku Klux Klan. It also epitomizes the Mulder- Scully Relationship. The MSR of the series is the heart of the show.
Humbug written by Darin Morgan is the most perfect hour of television to take the viewer on the journey from seeing Scully’s perception of the other to having the perception of the other looking at Mulder. Anyone interested in diversity or perceptions of disability should watch this episode whether they are X Files fans or not. Also, as the first comedic episode, it changed the series by inserting a more flexible framework for its storytelling.
Paperhearts written by Vince Gilligan also has a magic touch on a horrifically dark subject matter. The acting by David Duchovny is incredible. It’s heartbreaking.
Duane Barry written by Chris Carter and Ascension written by Paul Brown are action packed. Hostage situation, a kidnapping, Fox Mulder on the top of a moving tram, Scully abducted, Mulder in a speedo. It also begins the mythology arc which led the procedural series to experiment with what would become known as long form television.
The Sixth Extinction trilogy episodes were written by Chris Carter with Frank Spotnitz cowriting Biogenesis and David Duchovny cowriting Amir Fati. They are visually stunning episodes. I like the way they tie together but are each is so different. The episodes feature stellar acting performances by Duchovny and Anderson. The dream sequence writing by Duchovny is complex and intricate. There is a native mysticism sub plot, a Diane Fowler redemption arc, a Skinner compromised component, a man appearing to Scully, spaceships with scriptures, locusts, mind reading, you can chew on these episodes for day. They are meaty.
Requiem ends season seven. Duchovny will be in half the episode in season eight. He will return only in the finale for season 9. It’s the end of the series as we knew it and it’s done well with a recall to the pilot. With MSR leveling up,, Mulder gets abducted and Scully is pregnant and the X Files are being shut down for the mundane reason of a financial audit. It needed to be an episode which respectfully ended the status quo and begins a pivot and this episode did that well.
The Lost Art of Forehead Sweat by Darin Morgan is just a perfect farewell to the series and a perfect commentary on our time. It’s the perfect revival episode.
Grotesque, written by Howard Gordon, might seem unexpected but it’s creepy, it has amazing use of colors and shadows and it’s a great acting performance by Duchovny. It took me a while to love it but it has become a favorite.
Hollywood AD by David Duchovny would never have made my top ten even a few years ago. I thought it tried to do too much. Now I think it was written and directed with intentionality knowing people would watch multiple times. It’s foretold in Scully asking Mulder how many times he had watched a specific science fiction movie. There is so much layering in this episode that it would be impossible to comprehend it all in one setting and so I look forward to seeing something new every time. No one writes MSR like Duchovny.
Finally Within and Without both written by Chris Carter makes the list because Gillian Anderson does her best work in the series in these two episodes.
It is also not lost on me how many of the 13 episodes were directed by Kim Manners and Rob Bowman.
I can’t even say this is a best of list because I have applied no objectivity. I would be shocked if anyone else’s list looks similar. This a best loved list, my favorites for my own reasons. It is bound to change within the next ten years.