THE X-FILES Mythology Guide – Season 3


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“The Truth is Out There”


Season 3 picks up where the second season’s finale cliffhanger left off revealing that Mulder is still alive and seeing Melissa Scully murdered by Krycek and his partner, thinking that she’s her sister. It offers up some key mythology episodes which clarify various elements of the government conspiracy that have been developed so far. It also serves to deepen Mulder’s personal connection to the X-Files revealing that his family history has more in connection with the main conspiracy than just his sister’s abduction.

This season’s mythology greatly expands on the core ideas of the show and its characters’ histories, taking us back to the roots of the alien conspiracy. The abduction of Mulder’s sister is explained further, what happened during Scully’s abduction hinted at and the strange “Black Oil” alien life-form introduced for the first time.

Season 3 – What we learn


 In terms of understanding the main myth-arc better things kick off with Mulder discovering his father’s involvement in “The Project”. Bill Mulder’s working relationship with the Cigarette Smoking Man, and CSM’s relationship with the Mulders is also brought into the spotlight this season, highlighting the fact that Mulder’s nemesis has known him since childhood.

It turns out that Bill Mulder, CSM and some familiar faces including the Well-Manicured Man and Deep Throat, were part of “Operation Paper Clip” which saw Nazi scientists employed by the US to create alien/human hybrids following the Roswell crash. Smallpox vaccinations were used as a cover to collect genetic data from millions of US citizens for their experiments, the data hidden in the labyrinthine tunnels of an abandoned mining facility. The Well-Manicured Man tells Mulder that his Sister was abducted to prevent Bill Mulder from exposing the project. According to his mother it could have been him but his father chose Samantha to be the one that was taken. The information found in the mining facility files suggests that it was meant to be him at first as Mulder finds a file, originally labelled with his name, containing tissue samples from his Sister.

Later in the season it is implied that CSM had an affair with Teena Mulder, bringing in to question Mulder and his Sister Samantha’s parentage, a question mark that’s left hanging.

All these revelations stem from Mulder coming into possession of a digital tape containing the government’s secret files on alien activity on Earth in the past season. In a battle between the Syndicate and Mulder to get their hands on the tape, it’s the betrayed Krycek who ultimately acquires it. Rather than using it as leverage he sells secrets from the tape, with one in particular proving a crucial part of the season’s mythology. The tape contains details of a location in the Pacific Ocean where a UFO lies, downed in World War II by US fighter planes, along with a P-51 Mustang.


A ship called the Talapus retrieves the alien spacecraft while a member of the French salvage ship the Piper Maru is infected with an alien life-form, the Black Oil, as he discovers the US plane with its pilot trapped within, apparently still alive, at the same site. The Black Oil uses the bodies it enters for its own purpose destroying anyone who tries to hinder its progress. Prior to the events which take place in the current day, Bill Mulder and CSM investigated the first failed retrieval mission of the UFO in the 50s, which resulted in similar problems.

In conjunction with their investigation into an alien autopsy tape, which leads them to the Talapus, Mulder and Scully discover that Japanese scientists also have a part in the creation of alien/human hybrids. One of these scientists in particular is singled out as having been involved in Scully’s abduction, a Dr Zama. Not only does Scully recall having seen him during her abduction be he’s also responsible for making the chip that was implanted in the back of her neck.

Prior to this discovery Scully meets a group of women who are members of MUFON and have all had similar abduction experiences and have similar implants. They recognise her from “the bright white place” and forebodingly reveal that they’re all going to die from cancer caused by their abductions. Out of the group, one is dying of untreatable cancer, Betsy Hagopian, a name which will come up again in the series.

Aside from being in possession of the sought after digital tape, Krycek also becomes one of the hosts of the Black Oil on its journey from pilot in B-51 Mustang at the bottom of the Pacific to the recovered UFO. Passing from the pilot to the French diver Gauthier, then to his wife and finally to Krycek, the Black Oil returns to its ship which is contained in an abandoned missile silo.

At the season’s finale the Clone storyline is developed further with the introduction of Jeremiah Smith. Mulder and Scully are alerted to his presence when a man is claimed to have healed the victims of a shoot out at a fast food restaurant with only his hands. It’s not only Mulder and Scully who become interested in him, but CSM and the alien Bounty Hunter as well. CSM gets to him first however and it’s while he’s interrogating him that we first learn the date is set for alien colonisation (though what that date is is not mentioned), something which Smith’s rebellious actions have threatened to endanger. It’s also revealed by Jeremiah Smith that CSM has cancer, a fact which he uses to ensure his freedom.

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  1. WaySeeker says

    Thank you for these. I started watching the show on TV from the pilot! I have all the series on disc.
    They discovered the power of Myth-arcs as they ran the show. I think in season 1 or 2 they caught a glimpse. It was in Season 3 where they really put it out there, and saw how much it paid off (and how much they enjoyed doing it), so its really in season 3 with Myth-arc rubber hits the road, and they keep this up going forward.

    Like: Thumb up 1

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