Daily Dead’s Guide to the Essential Mythology Episodes of THE X-FILES

On Sunday, January 24th, Fox will bring back Chris Carter’s brilliant series, The X-Files, for a six-episode revival run that will reunite beloved FBI Special Agents Mulder (David Duchovny) and Scully (Gillian Anderson) for more alien-related exploits.

The last time we saw The X-Files on the airwaves during its initial run was back in May 2002, so if you watched the series throughout its nine seasons, you may be in need of a refresher on all the key players and integral storylines that make up the core mythology of The X-Files.

Mythology in regards to The X-Files could mean various things: the existence of aliens and how our government plays into that, various characters that fit in with different prophecies, the “Black Oil” that became a prominent antagonistic force during season three, the various conspirators and their attempts to derail Mulder and Scully’s work on the X-Files, Scully’s miracle child born during the eighth season, and whether or not the Cigarette Smoking Man was truly the devil incarnate or just another powerful opportunist.

In short, there’s a lot of stuff going on in The X-Files universe, which may seem daunting to revisit with the new revival less than two weeks away. Keeping that in mind, I put together this guide of essential mythology episodes worth watching before we meet up with Mulder and Scully again, so that you can help bridge any gaps you might have in your memory of the show.

For the most part, what you’ll read below is spoiler-free, so for all you newbies out there who may have never watched an episode of The X-Files but are curious about the upcoming limited series, this should also help you out in terms of seeing all the episodes that lay the foundations for the show’s ever-changing mythologies and lore.

“Pilot” (Season One, Episode 1)

When revisiting the past, it always makes sense to go back to where it all started. As expected, this episode sets up the X-Files division within the FBI, gives us some insight into both Mulder and Scully’s backgrounds, and also establishes the Cigarette Smoking Man as one of the biggest adversaries the new partners would face throughout the series.

“Deep Throat” (Season One, Episode 2)

This second episode furthered the overarching alien mythologies to The X-Files and also introduced viewers to Mulder’s initial informant, Deep Throat, who opened up the notion that there was a shadow government of sorts also involved with the X-Files.

“E.B.E” (Season One, Episode 17)

In this episode, Mulder and Scully are on the hunt for an E.B.E (extraterrestrial biological entity) that’s a pawn in a global conspiracy and is hidden inside a truck making its way across the US. We see in E.B.E that Deep Throat isn’t always working in Mulder’s favor, making it hard to determine the informant’s allegiances, and we’re also introduced to fan favorites The Lone Gunmen, who would come to figure prominently in future seasons (and would get their own spin-off series as well).

“The Erlenmeyer Flask” (Season One, Episode 24)

“The Erlenmeyer Flask” is arguably one of The X-Files’ best episodes, providing us with more information on the series’ ongoing alien-related mythologies. It also involves a major character moment for Mulder’s informant Deep Throat, and fans are introduced to one of the series’ deadly assassins, the Crew Cut Man, who would pop up in future episodes from time to time.

“Little Green Men” (Season Two, Episode 1)

Beyond just being a great hour of television, this season two premiere episode was notable for a few reasons. It features our first-ever glimpse of an actual “alien being” on the show, we see Mulder’s faith in his mission to uncover the truth shaken to its core for the first time, we’re given a glimpse into what happened the night Samantha Mulder was abducted, and we’re also introduced to Senator Richard Matheson (a nod to the famed writer), who would figure into later storylines.

“Duane Barry” / “Ascension” (Season Two, Episodes 5 & 6)

“Duane Barry” and “Ascension” formed a two-part episode arc revolving around Scully’s abduction, which gave the then-pregnant Anderson the opportunity to take some much-needed time off from the show (“DB” was also Chris Carter’s first episode as a director). The story centered on a hostage situation initiated by a disturbed man named Duane Barry who believes he was once abducted. Mulder is brought in to talk him off the proverbial ledge. Things go wrong, Duane eventually kidnaps Scully, and we see for the first time just how deep the loyalty is between Mulder and his partner when he can’t save Scully in time and we witness his emotional response to the loss of Scully at the conclusion.

These episodes essentially set up the oncoming Scully cancer storyline that factors into subsequent seasons, and it’s also worth noting that Steve Railsback as Duane Barry is an absolute powerhouse. Anderson would then return just two episodes later in “One Breath.”

“Colony” / “End Game” (Season Two, Episodes 16 & 17)

In this next two-parter (The X-Files made this type of format an art form all its own throughout its run), viewers were introduced to the idea of a covert cloning program and we also learn that Mulder’s sister Samantha may be involved with the aforementioned program. It’s during “Colony” that we’re introduced to another iconic series assassin, the Alien Bounty Hunter (Fright Night 2’s Brian Thompson), who would also become a notable baddie throughout The X-Files. Additionally, this story arc in particular bonded Mulder and Scully closer together than we had seen them before.

“Anasazi” (Season Two, Episode 25)

Easily one of my favorite X-Files episodes ever, “Anasazi” explores the depths of the conspiracy against our favorite FBI agents when a tape containing an encrypted Navajo code with damning evidence against the Syndicate is discovered, and the secrets it contains may come at a hefty price for both of the show’s heroes.

“Anasazi” also lays down some important groundwork to the show’s ever-expanding mythologies and puts both Mulder and Scully’s careers and their lives in serious jeopardy as well. This season two finale also introduces us to Navajo elder Albert Hosteen (the lovely Floyd Westerman), who becomes an important figure in Mulder’s life and is tasked with breaking the code. During a heartbreaking moment, we also see just how dastardly Alex Krycek (the FBI agent originally brought in tof replace Scully during her abduction) truly is after he kills someone near and dear to Mulder. The episode ends shockingly enough with the Cigarette Smoking Man demonstrating the lengths he will go to in order to keep some secrets buried.

“The Blessing Way” / “Paper Clip” (Season Three, Episodes 1 & 2)

These two episodes are a continuation of “Anasazi” and raise the emotional stakes Mulder and Scully have in investigating the truth behind the abductions to an entirely new level. The information contained on the encrypted tape comes heavily into play and in the latter episode, we learn some shocking truths about the Mulder children and also see just whose side Assistant Director Walter Skinner (Mitch Pileggi) is on after we’ve been led to suspect him of trying to subvert Mulder and Scully’s work in the past. “Paper Clip” is easily one of my favorite “Skinner episodes” from the entire X-Files series.

“Nisei” / “731” (Season Three, Episodes 9 & 10)

“Nisei” is one of the first episodes that heavily plays into the ramifications of Scully’s abduction during season two. Its story was heavily influenced by the atrocities performed by Japan on their prisoners of war during World War II. The way Carter interweaves his fictional mythology into this real-life tragedy is masterful and raised the stakes once again for both Mulder and Scully.

In the second part of this story arc, it is revealed that the idea of alien abduction may be a smokescreen for a larger conspiracy orchestrated by the shadow government known as the Syndicate—a conspiracy somehow related to Scully’s previous disappearance.

“Piper Maru” / “Apocrypha” (Season Three, Episodes 15 & 16)

These two episodes introduced us to the “Black Oil”, the alien substance that takes over its host and can infect anyone—a story element that would factor largely into the ongoing alien mythologies and would also be a key element to the (then) upcoming X-Files feature film.

“Apocrypha’s” final moments were a real shocker too, with some rather surprising revelations involving the Cigarette Smoking Man and his former associates. These episodes heavily involve Krycek and set up his character and his motivations for later episodes.

“Talitha Cumi” (Season Three, Episode 24)

This third season finale raised the stakes once again for The X-Files; it heavily focused on Mulder’s unrelenting quest to uncover the truth about the Syndicate and his family, while also grappling with Carter’s own reservations about how science had impeded our lives at that point. It ends on one of the series’ best cliffhangers, which would go on to be resolved in the first episode of season four.

“Herrenvolk” (Season Four, Episode 1)

“Herrenvolk” was a game-changing episode for a lot of reasons; we say goodbye to a beloved character, we are introduced to a new potential ally for Mulder by way of Marita Covarrubias (Laurie Holden), and Carter’s script also furthered the mythology of the cloned bees, which would also come to factor heavily into both the series and in the first X-Files feature film. We also learn that the Cigarette Smoking Man is a far more complicated villain than just a guy looking to destroy Mulder professionally, raising a few more questions that would get explored during the rest of season four.

“Tunguska” / “Terma” (Season Four, Episodes 8 & 9)

“Tunguska” and “Terma” was another two-part affair from The X-Files that dug deeper into the whole Black Oil mythology and took our beloved Mulder to Russia (alongside the nefarious Krycek) to explore the horrors of unmonitored scientific testing. The final shot of “Tunguska” is seriously the stuff nightmares are made of and we learn in “Terma” that Krycek is a guy who will play all sides against each other in an effort to get what he ultimately wants.

“Paper Hearts” (Season Four, Episode 10)

“Paper Hearts” isn’t necessarily a canon X-Files episode, but it’s worth mentioning anyway for several reasons. It features an incredible performance from Tom Noonan, it factors into the ongoing Samantha Mulder storyline, and its finale is amongst one of the series’ most gut-wrenching moments ever.

“Memento Mori” (Season Four, Episode 14)

“Memento Mori” is one of several character-changing episodes for Scully, as she is diagnosed with cancer that is related to when she was abducted back in season two. There is also more information revealed on how the cloning subplot to the X-Files plays into everything—an important element in upcoming episodes.

One of the reasons I personally adore “MM” is because we see how Scully’s diagnosis deeply affects everyone around her. For the first time, we see Scully let her guard down and watch as she struggles with her own faith and belief system, something that was heartbreaking and makes for absolutely compelling television. Anderson would go on to win a primetime Emmy for her work in “Memento Mori.”

“Zero Sum” (Season Four, Episode 21)

“Zero Sum” was another great Skinner episode that involved him in some of the show’s growing conspiracies and once again pitted him against the Cigarette Smoking Man (anytime Mitch Pileggi and William B. Davis shared the screen, it was magic). We saw the return of the deadly bees from “Herrenvolk” and also learned the truth about one of Mulder’s informants.

“Gethsemane” (Season Four, Episode 24)

“Gethsemane” is an odd beast of a season finale; it tried to shock viewers by inferring that Agent Mulder committed suicide (there was an impending movie at this point, so I don’t think a single fan bought it), which made it feel much more underwhelming than some of its predecessors. It does shake Mulder’s belief system to its very core with several revelations, making it an important episode that would set up what was to come in future seasons.

“Redux” / “Redux II” (Season Five, Episodes 1 & 2)

Both “Redux” and “Redux II” wrapped up the story from season four’s finale and tried their best to right the wrong of attempting to make fans believe Mulder would actually kill himself. These episodes also tackle the popular “alien autopsy” videos that were all the rage in the 1990s in a rather befitting way, considering Mulder’s now lack of faith in the existence of alien life. They also shook up the show’s own mythologies and revealed that someone within the FBI had been working against Mulder and Scully, hoping to discredit them and their work. We also get some intriguing news about Scully’s cancer diagnosis.

“Patient X” / “The Red and the Black” (Season Five, Episodes 13 & 14)

“Patient X” and “The Red and the Black” comprised another remarkable two-parter that established two important characters for later seasons of The X-Files—Agent Jeffrey Spender (Chris Owens) and his mother, Cassandra (Veronica Cartwright). The latter was an alien abductee who forces Mulder to let go of some of his doubts surrounding the existence of extraterrestrials, and also shares an important relationship with another key character in the X-Files universe.

The show managed to evoke some incredibly powerful images over the years, but it’s in these two episodes where we encounter the faceless Bounty Hunters—some of the most menacing versions of these assassins we would ever see. These two episodes also heavily establish the concept of alien/human hybrids and explore the concept of alien colonization here on Earth.

“The End” (Season Five, Episode 20)

“The End” was originally supposed to be just that—the end of The X-Files as a television series. Carter had wanted to continue the adventures of both Mulder and Scully on the big screen from this point on, but Fox realized the show was still a huge cornerstone to their programming and negotiated its return. It ended up being a pivotal episode for more than just its foreboding name—certain truths are revealed, we see Mulder’s iconic office go up in flames and it introduces us to Diana Fowley (Mimi Rogers), a key figure from Mulder’s past as well as the adorable Gibson Praise (Jeff Gulka), who may just be the key to everything contained within the X-Files.

“The Beginning” (Season Six, Episode 1)

“The Beginning” was one of the more frustrating season premieres for me as a fan, because we watch both Mulder and Scully get ousted from their specialized division and see it taken over by two of the most conniving agents to ever walk the halls of the FBI. “The Beginning” was also the start of a new era for the series (production moved from Vancouver to Los Angeles at this point) and does its best to tie up some loose ends with the Gibson Praise storyline as well as some key elements from the X-Files feature film that had been released during the previous summer.

Overall, not one of the stronger premieres, but it is an important episode nonetheless.

“Two Fathers” / “One Son” (Season Six, Episodes 11 & 12)

“Two Fathers” / “One Son” wrapped up the Cassandra Spender story arc established earlier in the season in some rather nifty and intriguing ways. We see the Syndicate tested for the first time ever in series history during this two-parter, and co-writers Carter and Frank Spotnitz further explored the alien/human hybrid storyline. Audiences were also once again reminded that the morphing alien rebels were still as dangerous as ever and that Krycek will literally double-cross anything with a pulse.

“One Son” served as a relaunch for The X-Files in many ways (none I’ll spoil here) and also filled in some important plot points relevant to questions raised during earlier seasons involving Mulder’s father and his sister Samantha’s disappearance. The episode’s final moments were a real doozy—honestly, this was the last time during this season when I felt emotionally invested with the show.

“Biogenesis” (Season Six, Episode 22)

If I’m being honest, “Biogenesis” (as well as the next two episodes) was kind of a wash for me as a fan back when the series was in its first run. I wasn’t a huge fan of Carter rewriting his own mythologies, taking a bit of a theological approach to the existence of aliens and how they played into the creation of God and affected humankind millennia ago (sounds a bit Prometheus-y, yes?). That being said, I’ve warmed up to it over the years and it’s absolutely a key episode to The X-Files’ ever-adapting mythology.

“The Sixth Extinction” / “The Sixth Extinction II: Amor Fati” (Season Seven, Episodes 1 & 2)

At this point in The X-Files’ nine-season run, Carter knew he had to mix things up a bit and he definitely does with both “The Sixth Extinction” and “Amor Fati” which, again, weren’t my favorite episodes by any means, but they do help further along some new mythologies, contain several huge reveals pertaining to both Mulder and Scully, and tie up a few character storylines as well.

“Sein und Zeit” / “Closure” (Season Seven, Episodes 10 & 11)

Get those hankies ready, because “Sein und Zeit” and “Closure” combined for a season seven two-parter that finally gave us some answers about what happened to Samantha Mulder all those years ago, and they pack a huge, emotional wallop. This story may not necessarily make a lot of sense in relation to several revelations learned about Samantha in previous seasons, but these episodes felt like a necessity in making the character of Mulder more than a guy moping around looking for his lost sister after all these years.

Also, the last few minutes of “Closure” feature some of the best work Duchovny ever put in on the series. Wonderful stuff, even if it didn’t necessarily work 100% story-wise.

“Requiem” (Season Seven, Episode 22)

With his impending departure from the show, “Requiem” is also known fondly amongst X-Philes as the “Mulder Abduction Episode”, because we see our hero taken away by extraterrestrials just as he finally puts together some of the most important pieces to the alien puzzle he had so long tried to solve. “Requiem” also ends with another shocker: the news that Scully is pregnant—an unexpected reveal since she had been told in a previous episode that she was unable to conceive.

“Requiem” is a bit bumpy, but I enjoy it for the simple fact that it cleverly incorporates some concepts from the “Pilot” episode and proved that Carter still had the ability to keep fans on their toes even after 160+ episodes. I believe it was also the last time we’d see Cigarette Smoking Man until season nine.

“Within” / “Without” (Season Eight, Episodes 1 & 2)

With Duchovny now officially departed from The X-Files in any sort of full-time capacity, it was up to “Within” and “Without” to act as a bridge for fans by giving us some resolution to the details of Mulder’s abduction and also doing its best to introduce us to the “new sheriff in town”, Agent Doggett (played by Robert Patrick).

“Within” is also notable for the return of Gibson Praise and the beginning of The X-Files’ ongoing exploration of the themes of resurrection and rebirth. Some of its events would go on to directly tie into the final season’s first episode as well.  “Without” is a standout episode strictly due to its surrealistic nature and the haunting image of Mulder being held captive as Alien Bounty Hunters look on.

“Per Manum” (Season Eight, Episode 13)

“Per Manum” digs into Scully’s unexpected pregnancy a bit deeper when she investigates a case involving a woman who gave birth to an alien fetus. The story plays out like Rosemary’s Baby served up with a sci-fi twist, provides us with some Mulder scenes via flashback, and was a great showcase for Anderson overall.

“This is Not Happening” / “Deadalive” (Season Eight, Episodes 14 & 15)

“This is Not Happening” and “Deadalive” both focus on the return and resurrection of Agent Mulder, as Scully and Doggett finally discover his body in the woods alongside several other abductees. We see Skinner get tested in unimaginable ways by Krycek and also see the return of Billy Miles, who factored heavily into the series premiere. “Deadalive” (a reference to the Peter Jackson movie) teases fans with Mulder’s funeral, but as expected, it’s hard to keep a good FBI agent down. It’s also worth noting that these episodes have some killer special effects and we get the introduction of Monica Reyes (Annabeth Gish) in this two-parter, too.

“Essence” / “Existence” (Season Eight, Episodes 20 & 21)

The final two episodes of season eight, “Essence” and “Existence”, were penultimate for several reasons, as we saw longtime allegiances switch as well as the birth of Scully’s child, which would set up an important subplot for the ninth and final season of The X-Files. And for all the shippers out there, Mulder and Scully finally kiss after eight long seasons of “will they or won’t they?” This two-parter also furthered the Super Soldier storyline, which eventually has implications on the future of Scully’s newborn son.

With The X-Files’ future uncertain, these episodes were also designed to tie up loose ends, while also leaving some possibility for potential stories as well.

“Nothing Important Happened Today”, Parts I & II (Season Nine, Episodes 1 & 2)

Season nine was around the time where things for The X-Files felt a bit disjointed to me as a fan. It seemed like Carter struggled to give the long-running series a new direction to go in with Duchovny officially gone, as some of the overarching mythologies got a bit muddled up towards the end.

That being said, these first two episodes of what would become the final run for The X-Files effectively set up the continued plot around Scully’s baby, William. “Nothing Important Happened Today” also hearkened the arrivals of Cary Elwes as Brad Follmer and Lucy Lawless as the mysterious Shannon McMahon (who was supposed to be featured more but had to depart the show due to her pregnancy).

“Provenance” / “Providence” (Season Nine, Episode 9 & 10)

Both “Provenance” and “Providence” have their good and bad moments, but it’s a noteworthy two-parter in that it brings back the mythology surrounding the alien rubbings from season six’s finale, “Biogenesis”, and also introduces us to the Toothpick Man (Alan Dale), the new leader of the Syndicate who has a few secrets of his own.

Both episodes also further establish the mystery surrounding William and explain how he relates to the alien colonist prophecy that has evolved throughout the last few seasons. And considering that there’s been talk of William’s fate being addressed already in a lot of the promotional talks for the new mini-season of The X-Files, these two episodes seem well worth revisiting now.

“William” (Season Nine, Episode 16)

Directed by Duchovny, this is the episode in which Scully makes the ultimate sacrifice in order to ensure the safety of her son, William. We see the return of a sort of familiar face who informs Scully of a prophecy involving the newborn, and while some of it feels off character-wise, “William” is definitely an important episode nonetheless.

“The Truth” (Season Nine, Series Finale)

Well, if you’re going to start at the beginning, then clearly you should finish with the end, no? “The Truth” was the two-hour series finale of The X-Files that brought Mulder back for one final hurrah and addressed the impending alien invasion first revealed in season two.

“The Truth” wasn’t nearly as monumental as I had hoped when I first watched it, due to the fact that it raised a few new questions that ultimately still have yet to be answered. When I revisited it last year, though, I enjoyed it much more and loved how Carter and all those involved came together to give us fans their very best attempt at a sendoff befitting of both Mulder and Scully. Lots of beloved past characters pop up during “The Truth” as well—some expected, and some very unexpected.