I've mentioned before The X-Files' tendency to give-and-take with the revelations it offers the audience. Furthermore, as embodied in the vital conflict between Mulder's belief and Scully's skepticism, a lot of what we see vis-à-vis extraterrestrial life is not free from critical doubt - and it's not as though this series doesn't condition the audience to be paranoid, to the point of even doubting their own suspicions about what the government may be covering up. This factor is played upon to excellent effect in the fourth season finale revelation that I keep referencing. At the risk of spoiling it now (it goes to show how provocative it is that I can't wait - although I've tried - until I've rewatched the episode to talk about it), the central question that the revelation brings up is this: everything that we've seen so far, is it all just an elaborate hoax?
And The X-Files does a pretty good job of carefully rationing out the evidence, such that even after seeing so much (and this might go a long way in explaining Scully's stubborn skepticism), the audience can still hold on to a doubt in the back of their minds that any of it is genuine. For example, we don't know if it was actually aliens that abducted Scully in Ascension, or just the government. Even the alien abductions in the pilot episode itself are not conclusive. Granted, some of the evidence is harder to discredit than others. So far, one of the most convincing examples is in just the second episode of the series, Deep Throat, when Mulder witnesses up close a military aircraft with unbelievable technical capabilities. Still, who can say that top secret military technology is not just that far advanced beyond what the public knows about? How can you say without a doubt that the technology is truly extraterrestrial in origin?
Then you have things like the alien fetus Scully sees in the first season finale, The Erlenmeyer Flask. This is pretty damning evidence, but can you say with 100% certainty that it's not a fake? Indeed, that's what turns out to be the case with the discovery in the fourth season finale. True, it's hard to believe a hoax that turns out to be as elaborate as the conspiracy itself - if not more so. If ever there was a reason to believe, it's the incredulity of the notion that the government would be so invested in having people believe in extraterrestrials (to which end their conspicuously total denial would ostensibly serve), that they would go to the trouble of fabricating so much false evidence. What would they have to gain from this absurd belief? Yet E.B.E. is a perfect example of this. This episode is so highly suggestive, and yet, unlike The Erlenmeyer Flask, nothing is revealed in the end, except for an empty bed. This is the episode in which Deep Throat even admits to lying to Mulder and fabricating fake evidence in order to lead him on!
But, of course, this being The X-Files, it's safe to assume that there will really be aliens involved in the end. And, crucially, it's the scientific stuff that best holds up to scrutiny. Like when Scully gets confirmation from a chemist in The Erlenmeyer Flask (who is subsequently killed, and the evidence confiscated) of living tissue that matches nothing on this Earth. Then there is the shape-shifting Alien Bounty Hunter in Colony/End Game. While it can't be concluded that he really is an alien (he never appears in any form other than human) - and who's to say that the clones are really alien/human hybrids and not just fallout from Russian genetic experiments, as the CIA agent claims (who probably, but not definitely, was the Alien Bounty Hunter in disguise) - his remarkable ability to shape-shift, and the nature of his toxic, green blood (not to mention his imperviousness to bullets), is highly suggestive of an extraterrestrial explanation.
Finally, we come to the events of the season 2 finale. When The Thinker handed off the "MJ Documents" to Mulder in Anasazi, he prefaced them in such a way as to lead us (both Mulder and the audience) to believe that they contained information about the government's contact with extraterrestrial life. And what we saw of the conspirators' reaction to those documents being leaked confirmed that they were indeed genuine, and of a particularly sensitive nature. But, being encrypted in Navajo, the documents require some effort to be translated. Even allowing for the fact that The Thinker was a genius hacker, and may have been up to the task of cracking the code, he himself admitted that he had not had much time to look them over, as he knew as soon as he got them that the government would be after him.
Yet, what little information Scully and Albert Hosteen were able to interpret from the documents pointed not to alien subjects, but to a series of human (or rather, inhumane) experiments conducted during or after WWII - which, though not as groundbreaking as evidence of extraterrestrial contact, could very well account for the behavior of the conspirators (even Mulder's father). What modern day agent of the state would want it found out that his government (if not he, himself) had been directly involved in the kind of sick experiments the Nazis were known for? Especially if he (and that government) were still involved in similar experiments to this day! Now, the tantalizing possibility that what we're dealing with is experiments that involve alien-human hybrids - in a sense, testing on humans using alien DNA, like what was done in Red Museum - has been suggested. But can we be sure?
The answer to that question is no. It may yet prove to be the case. But, if I'm not mistaken - and this discussion may ultimately turn out to be moot, when and if this issue is eventually resolved - evidence from a later mythology episode may point to a different, and rather more terrestrial (if not less horrifying), explanation. At the same time, all of the conspirators' reactions are justified, regardless of whether the explanation goes one way or the other. It just goes to show that in this series, you can never be too sure of anything. There is always doubt, which engenders a lot of paranoia, and one can never be completely sure that anything of real substance has been discovered - anything that can be taken to the media and used to blow the lid off this whole conspiracy. It results in a good deal of confusion, no doubt, and I'm sure this is the cause of many fans' disillusionment with the mythology of the show. But I'm not sure it's an example of excessive retconning so much as a deliberately subtle and careful rationing of information, some of it intentionally deceptive, in a fictional (yet not so unrealistic) world where no one can be trusted.
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