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X-FILES Declassified: Alien Mythology and Government Conspiracy

I never thought we’d be in a world where The X-Files would return to our screens, much less one everyone was excited about. And yet, it’s happened, and the joy surrounding the reunion of Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson), even for just six weeks, has me reliving my love of the series which never failed to terrify and intrigue while asserting “the truth is out there.”

In celebration of the series and its six-week return, we’re taking a look at the returning writers who all helped shape the original series, which ran from 1993 to 2002. Glen Morgan, James Wong, and Darin Morgan are all contributing “monster-of-the-week” episodes to the revival, and creator Chris Carter has grabbed three for himself. And since the first episode was a heavy alien mytharc episode, I’ve decided to start with Carter’s mythology episodes from the first several seasons.


Chris Carter wrote several episodes every season, but it’s interesting to note that, for the first few years, he only wrote a couple mythology episodes himself. In season 1, for instance, he only wrote the “Pilot,” the second episode “Deep Throat,” and the finale, “The Erlenmeyer Flask.” These detailed Scully’s “promotion” to the X-Files in order to debunk Agent Mulder, who is a crazy person, yes, but is also very close to finding the truth about something. The pilot shows us the now-infamous Cigarette Smoking Man (William B. Davis) who would go on to factor into the conspiracy narrative and become the show’s de-facto main villain. The second episode introduces Mulder’s shady government contact, known as Deep Throat (Jerry Hardin), who popped up throughout the first season to push Mulder in the right direction.

The most important myth arc episode in the first season, though, is definitely “The Erlenmeyer Flask.” That episode not only kills off Deep Throat but insinuates at the larger conspiracy within the government even further. It also shows evidence, in the form of a warehouse full of alien fetuses (or possibly just mutated human fetuses), and how quickly that evidence can disappear if the shadow government wants to make it so. The episode also set up the recurring theme of the FBI shutting down the X-Files on occasion, and whether Assistant Director Walter Skinner (Mitch Pileggi) is on the side of the angels, as it were.


Season two really upped the ante on the alien myth arc plot and established that, for the most part, the mythology plot episodes were among the series’ highlights. The second season is also the only one to have a premiere written by someone other than Chris Carter, in this case “Little Green Men” written by James Wong & Glen Morgan. I’ll talk more about that episode next week, but it set up Mulder and Scully being apart for the first several episodes, with Mulder conducting his paranormal investigating on the down-low. This season also introduced Agent Alex Krychek (Nicholas Lea) who is working for the conspiracy and then becomes a free-wheeling agent of chaos.

Carter’s first mythology episode of season two is the powerhouse “Duane Barry,” in which a crazed man (played by guest actor Steve Railsback) takes an office hostage blathering on about alien abduction, and Mulder has to negotiate with him. It’s a deeply tense episode where Mulder plays hands he isn’t sure about, and how much he lets Barry believe he believes gets him in hot water with the higher-ups. At the end of this episode, Barry escapes and finds Agent Scully and kidnaps her so she can take his place as an offering to “Them,” which is followed-up in the next episode.

Later, Carter wrote the episode “Red Museum” in which a cult of vegetarians is believed to be “walk-ins,” or people whose souls are inhabiting other bodies. However, it turns out to be evidence of inoculation against some unknown disease, possibly alien in origin.


One of my very favorites of the season is “Colony” which was co-written by Carter and Duchovny. It introduces the idea of Mulder’s sister, who he believes was abducted by aliens in front of him as a child, actually being alive and well and a grown up. But it also introduces the concept of the alien shape-shifters, which would become one of the major alien races in the show, along with the shape-shifting alien bounty hunter (Brian Thompson). He himself an alien but goes around stabbing other, untrustworthy aliens in the base of the neck which causes them to melt and ooze green slime. It’s pretty badass.

Leading into the following season, Carter wrote the season two finale “Anasazi” and the two-part season three premiere “The Blessing Way” and “Paper Clip” which all deal with a digital tape that has evidence of the conspiracy on it. It also finds Mulder trapped inside a train car buried in the desert with tiny beings which he believes are (and, come on, they probably are) aliens, of the grey variety. This continues the inoculation subplot which says the smallpox vaccine in the ’50s was actually a test about the alien pathogen called Operation Paper Clip. Mulder is also wounded and near death but is brought back to life by Native American shamanism. That bit’s kinda weird.

Season 3 really kicks the conspiracy mythology into high gear with Carter co-writing a further pair of two-parters; “Nisei” and “731” which detail Japanese involvement in alien experimentation aboard trains (sidebar: look up Unit 731 and read about the horrible atrocities Japanese scientists performed during WWII), and the big ones, “Piper Maru” and “Apocrypha.” These introduce the other big alien species on the show, the black oil which infects people and is seen floating around their eyes. It’s maybe the best and most consistent aspect of the show’s myth arc.


Carter usually paired with writer Frank Spotnitz for the mythology episodes in season 4. In this season especially, the effects of Scully’s abduction in season 2 become more apparent, including her ultimate realization that she has the same strange, inexplicable cancer that has befallen several other women who were abducted. It also furthers the idea that Mulder is both a liability to the FBI and an asset, and cements AD Skinner as a true ally, though a gruff and by-the-book one. Throughout the show, there were several informant characters, starting with Deep Throat in season 1, Mr. X (Steven Williams) in seasons 2 and 3, and finally Marita Covarrubias (Laurie Holden) in season 4 who popped up throughout the rest of the show.

Carter’s alien mythology for the show came to its planned end in season 5, with the first feature film in 1998 meant to serve as the show’s finale. However, since the show’s ratings were so high, the pressure from Fox to keep it going meant that they had to stretch things a bit. The alien mythology never again reached the pinnacle it did during those first few years, especially 2-4. But we’ll talk more about the later Chris Carter-penned alien mythology episodes in a few weeks.

Next week’s episode of the miniseries is written and directed by James Wong. He wrote for the show in its early days, almost always partnered with Glen Morgan, who has his own episode later on. So, next week, I’ll talk a little bit about Wong & Morgan’s contributions to the show, which yielded some of the The X-Files‘ most classic episodes.

Let me know your favorite Chris Carter alien mythology episodes in the comments below!

Images: Fox Television/Ten Thirteen Productions

Kyle Anderson is the Weekend Editor and a film and TV critic for The X-Files was the very first TV show he was obsessed with  and he has watched it all a number of times. He considers this not a waste of time in the least. Talk to him about the show on Twitter!

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