Before reading the list, keep these facts in mind. This is my personal list, so there will be things you disagree about. I tried to have a combination of mytharc, standalone, funny, and serious episodes. It’s completely subjective, so the order or even the episodes on the list may not make sense for you.
25. Trust No 1 (Season 9)
I am hesitant to add any season 9 episodes to the list since the last two season were terrible. Instead of trying to tie up the various threads the previous seven seasons started, the writers created the super soldier arc which muddled the situation even more. ‘Trust No 1” was an episode focusing on Scully which meant lots of great acting by Gillian Anderson – always a plus – and the story was decent, so I think it deserves a spot on the list.
24. Requiem (Season 7)
The X-Files went all the way back to the beginning with Mulder and Scully returning to Bellefleur, Oregon where they first investigated a case. Many characters were brought back which was nice. In some ways, it was as if The X-Files finally found its way back after wandering through the wilderness for 40 years. I thought this episode set up great potential for season 8 which didn’t work out in the end. Either ways, “Requeim” had fantastic acting and a decent story. This also marks the last time David Duchovny was a regular on the show which forces me to put it on the list.
23. Paper Hearts (Season 4)
When Samantha is involved, Mulder immediately changes. He can be easy going all the time, but once Samantha’s abduction comes into play, he is reckless and loses perspective. That’s exactly what happens in “Paper Hearts.” Mulder is manipulated into believing that a serial killer had abducted her instead of aliens. In the end, it wasn’t true and no new information was discovered, but it’s all about the process of getting to that conclusion, and the episode hit it out of the park.
22. Triangle (Season 6)
Mulder goes off to the Bermuda Triangle looking for a ship, and instead travels back to 1939 where Nazis have taken over. The catch is that some of the people he meets look exactly like people he knows back home. Maybe it was a hallucination and never really happened, but that’s not the point; the episode was a blast.
21. The Erlenmeyer Flask (Season 1)
“Trust No One.” This simple phrase became the mantra of our heroes with the death of Deep Throat. The episode marks a transition where many parts of the government conspiracy become known with the alien blood, fetuses, and of course the Purity Control. Maybe one could argue that this is the start of the confusing stuff, but self-contained, the episode added a lot to the show, and gave us plenty of great stories later on.
20. Humbug (Season 2)
Sideshow freaks, underdeveloped fetus, and a general humorous tone to the episode. There was plenty of horror with the Fiji Mermaid, and yet the whole situation was funny. The weird combination made the episode lots of fun.
19. Monday (Season 6)
The concept for this episode isn’t original as it has been done multiple times in various mediums; however, that does not mean the various incarnations of the concept are bad. The concept of timeloops itself allow for great creative freedom which usually ends up with a good episode. The X-Files did it very well with several ongoing gags such as the waterbed leaking.
18. Pusher (Season 3)
The idea behind the episode was so good that Fringe copied the concept, having someone be able to control the mind of others. What was unique about Modell was that he was able to affect human physiology. He plays a cat and mouse game with Mulder, eventually baiting him into a sick game of Russian roulette with he, Mulder, and Scully.
17. How the Ghosts Stole Christmas (Season 6)
Everyone always say they like the episode for Lily Tomlin, but there are so many other reasons to like the episode. There’s Ed Asner, and a clever script. An endearing part of the episode was the mere fact that on Christmas Eve, Mulder would go ghost hunting, and trick Scully into coming. The first act is delightful to watch, and probably one of my favorite interaction between Mulder and Scully.
16. Deep Throat (Season 1)
I find this episode vastly underrated which I suspect is because it comes right after the pilot, and the pilot gets a lot more attention. “Deep Throat” further pushed the concept of Scully the Skeptic and Mulder the Believer, introduced their season one ally, and of course featured Seth Green as a pothead.
15. Squeeze/Tooms (Season 1)
Eugene Victor Tooms is one of the best monsters in The X-Files with his special ability to stretch and appetite for human liver. The story went away from the alien storyline, focusing on a totally separate issue. Surprisingly, it was the first monster-of-the-week episode, and it was very good. Usually shows may take a while to gain a footing, but Squeeze and later on Tooms set the standard for MOTWs to come.
14. Nisei/ 731 (Season 3)
Out of the earlier mytharc episodes, I think these are the most underrated. I felt that they conveyed tension perhaps better than any other episode with the stuff on the train and the events leading up to it. X showed another side, risking his life to save Mulder which only made his death feel worse. Like most X-Files episodes, we didn’t really no what was real or not it the end. There was the alien autopsy, lepers, Japanese, and it didn’t all fit together nicely. Eventually this made the show hard to digest, but in the beginning, it created intrigue and mystery.
13. Clyde Bruckman's Final Repose (Season 3)
When The X-Files does comedy, it’s never overt jokes with rich punch lines. It was a terrific episode with the hilariously fraudulent Stupendous Yappi, and Clyde Bruckman, played by Peter Boyle. It was dark episode -- talking of death can never be considered light -- but there was a fun off-beat tone that made the episode really great.
12. The Post-Modern Prometheus (Season 5)
I don’t know where Chris Carter came up with this idea, but those that call him a hack should watch this episode many times. Featuring The Great Mutato, a play on Frankenstein, the episode is black and white, and is heartwarming in the end. I guess in a way the episode is nonsensical with a couple ridiculous stories, but that is part of what makes The X-Files fun.
11. Memento Mori (Season 4)
The diary entries read by Scully are so chilling. David Duchovny is the one who gets the recognition for The X-Files, but when I think of the emotional scenes, I always think of Gillian Anderson, and the writers gave her a great role to play in the cancer arc. In a very emotionally charged episode, Mulder also had many great moments. There was more infiltration of private institutions with the doctor and random clones.
10. Bad Blood (Season 5)
Like “Jose Chung’s From Outer Space,” this episode showed differing perspectives from different people. This time, it was Mulder and Scully and their experiences after killing a “vampire.” They actually remember quite similar events, but the subtle differences in their behavior and appearances make the episode one of the most fun.
9. The Host (Season 1)
In terms of weirdness, the Flukeman certainly ranks up there. The science in science fiction amounted to making the connection to Chernobyl which while ludicrous, actually brought up an interesting idea. The episode had an unclean feeling with Mulder crawling around the New Jersey sewer system that made it disturbing and fun to watch.
8. Pilot (Season 1)
No list would be complete without the episode that started it all. It introduced the greatest team in television history (I’m looking at you Moonlighting fans!), alien abductions, and the government conspiracy. It’s a wonderful, wonderful initiation to the paranormal aura that is key to the show.
7. Duane Barry/ Ascension/One Breath (Season 2)
These three episodes didn’t air in order, but the forgettable episode “3” I think can be cast aside. These episodes raised the stakes of the series, getting Scully permanently involved in the conspiracy. Steve Railsback as Duane Barry was great, but out of those three, “One Breath” is the most memorable episode, and I believe on a totally different level than the other two. There is no alien activity or the usual X-Files fare. Instead it is a very personal and human episode, focusing on Scully and her inner struggle.
6. X-Cops (Season 7)
I love this episode so much. It combines the Fox shows, Cops and The X-Files to create an odd mix. We got to see the usual nightly hijinks you’d see on Cops, and a paranormal story. It felt authentically Cops, but there was Mulder, Scully, and a mystery. It was fun to see how the characters would react to being on national television. I still remember the scene where Mulder is talking to the an officer, explaining all about werewolves. The camera pans over to Scully who promptly hides behind the ambulance door. How great is that?
5. Home (Season 4)
This episode has to be one of the scariest episodes on television ever. Not only was it visually disturbing, but also it had the most horrendous, disgusting story. There were inbred things (they’re definitely not human) that impregnate their mother and go around killing people. Did I mention that the mother actually wanted to be impregnated? Glen Morgan and James Wong truly gave us a script riddled with everything wrong, and Kim Manners directed it perfectly. If there is one memorable X-Files episode that comes to the mind of everyone, it is always “Home.”
4. Gethsemane/ Redux/ Redux II (Season 5)
It’s interesting that the writers shaped the character of Mulder to be so dedicated to the pursuit of the truth of alien existence, that it is plausible that Mulder would kill himself over it. While that never happened, it makes you wonder if he would kill himself if that was 100% definitive proof that there wasn’t aliens. There was great acting by Gillian Anderson once again. I know it may seem redundant, but she’s amazing.
3. Beyond the Sea (Season 1)
Luther Lee Boggs is my personal favorite “monster.” He’s just a normal human who may or may not have psychic abilities, but his general creepiness and ability to mess with people’s minds without anything overtly supernatural makes him unique. Brad Dourif did a really terrific job in this episode, and his character is as memorable as any that have shown up on the show.
2. Anasazi/ The Blessing Way/Paper Clip (Season 2,3)
These episodes are probably my favorite set of mytharc episodes. Before the mythology got too complicated, we could actual understand something of what was going on. The breath and scope of the episode really impressed me. It had hacked classified information, Navajo code-talkers, a black helicopter incursion, Mulder almost dying and coming back, a standoff with Skinner, weird midget aliens, Krycek, and a great ending that characterizes all X-Files episodes.
1. Jose Chung's From Outer Space (Season 3)
This is my all-time favorite episode. From beginning to end, it is a laugh out loud episode, cleverly written with no real distinct stories. We know Mulder and something alien related is in the episode, but the rest is all out to the imagination of the viewer, or the various characters’ Jose Chung interviews. Charles Nelson Reilly who plays Chung was simply brilliant, and the idea behind the episode that he was brought back for an episode of Millennium, Chris Carter’s short lived show, in an equally good episode. There was also Jesse Ventura and Alex Trebek which added to the surreal tone of the episode.