The X-Files: The Shape of the Conspiracy - Part One: Sceptics and Secret Smokers

Carl Busch and Ronald Pakula - the assassin and the liar?

The "shape" of the conspiracy in the early episodes of The X-Files is actually remarkably simple. Mulder and Scully go out to investigate UFOs, and Mulder repeatedly stubs his toe against the US military, who are responsible (a) for recovering crashed alien spaceships and harvesting their technology and (b) for keeping this secret from the public - which explicitly is all for the sake of national security. Governments have the right to keep their military secrets under lock and key, after all, and the inference is left dangling that if the public were to find out that "we are not alone" there would be mass panic. And if that also means covering up that the aliens are abducting human children and doing obscene experiments on them then that's just too bad! (We later find out that the abductions in the first episode were actually all about turning humans into super-soldiers, so we can perhaps legitimately infer some background military interest there as well. But perhaps we're getting ahead of ourselves!)

All this is more or less confirmed later on. We find out in 'Redux' that in 1947 the Majestic 12 (MJ12) organisation was set up by the US Government to investigate the Roswell crash, and by inference we can connect the dots with other "military" episodes such as 'Deep Throat', 'Fallen Angel' (and its sequels 'Tempus Fugit' and 'Max'), 'E.B.E.', 'Little Green Men' and of course the 'Dreamland' episodes, in which we actually meet named MJ12 agent Morris Fletcher (not to mention his wife and children).

So far, so simple! No hybrids or clones, no Alien Bounty Hunters or Black Oil, no Syndicate or Rebel Colonists!

So, what then of the X-Files?

We're invited to imagine at the end of the pilot episode that Mulder's superiors at the FBI want to shut him down partly because they view him as an embarrassing crank who'll give the Bureau a bad name and partly because they see the X-Files themselves as a waste of money. It's only right at the end, with the appearance of the Smoking Man (the latterly named Carl Gerhard Busch, aka C.G.B. Spender) and his Spielbergian government warehouse in the bowels of the Pentagon, that we first get a suggestion that beyond the sceptics in the FBI there are other government agents out there who are actually rather interested in Mulder's work. The CSM clearly works for the Pentagon, who are apparently content for the time being to allow Mulder to investigate alien and/or "paranormal" activity on earth provided (a) it can all be kept under wraps and (b) they get to keep any physical evidence he discovers. (We see the Smoking Man filing away Ray Soames's tracking device, and in the first season's final episode he does the same with the alien foetus from Fort Marlene. And in the second season a not dissimilar fate awaits Dr Banton himself in 'Soft Light', thanks to Mulder's connexion with X - who is supposedly Mulder's contact at the Pentagon, not to mention his friend in the FBI, even though it's not always clear which of them is working for the other.)

In the second episode, the military situation is fleshed out, and we discover not only that the air force are flying their own UFOs but also that they're well up to date with the old government mind-control experiments. Indeed, they can pinch your most recent memories right out of your head if they want to. And we're introduced to another military secret agent who is also interested in Mulder's work and who, like the CSM, is also (we later learn) free to come and go at the J. Edgar Hoover Building.

In fact Deep Throat is even more interested in Mulder than the Smoking Man is. In fact he's willing to provide Mulder with inside information, the implication being that Ronald Pakula fancies himself as a latter day Mark Felt and that Mulder and (presumably) Scully are going to be his Woodward and Bernstein. He wants to expose the government conspiracy that he's been involved in "for a long, long time", but he'll need their credibility in order to do so. And he's well aware what will happen to him if he's caught.

For a few episodes at least, this arrangement holds. Deep Throat gives Mulder some scraps of background on a couple of military projects that people weren't supposed to know about (a mad computer, a creepy kiddy cloning programme, etc.*) He also winds him up something rotten by helping him land a couple of really big extraterrestrial fish (in 'Fallen Angel' and 'E.B.E.'). And he gets back... what exactly? It's worth bearing in mind that he initially approaches Mulder not to give him inside knowledge but to warn him off investigating Ellens Air Force Base. The quid pro quo may as well be that Mulder will get inside information provided he's prepared at times not to dig too deeply. So, is Deep Throat's job to control Mulder as much as it is to encourage him? (To be fair, that's often how UFO researchers have been treated by government agents in real life.) All we can say for certain is that he's testing and training Mulder and gaining both his trust (in a world where one should trust no one) and his personal loyalty (which, in a world of conspiracies within conspiracies, is an important thing).

We find out at the end of 'Fallen Angel' though that Pakula isn't just helping Mulder in secret. He's also protecting him from on high. When Section Chief McGrath asks him why he's protecting Mulder, he replies enigmatically

I appreciate your frustration, but you and I both know Mulder's work is a singular passion - poses a most unique dilemma. But his occasional insubordination is in the end, far less dangerous ... [t]han having him exposed to the wrong people. What he knows...what he thinks he knows... Always keep your friends close, Mr. McGrath... but keep your enemies closer.

By implication then, Pakula is telling Mulder that he's helping him to get at the truth whilst at the same time reassuring the FBI that it's better to keep Mulder on a short leash (or at the very least to have him inside the tent pissing out) - working under the supervision of a section chief (not to mention people like the Smoking Man), writing up X-Files that can then be safely buried away, and, of course, having Scully "spying" on him the whole time. Who are "the wrong people"? Again by implication (and it's a daring double bluff by Deep Throat) they're probably people like Deep Throat himself. (Of course, also by implication, Pakula is also admitting to McGrath that the military does indeed have secrets that it would be dangerous for Mulder to uncover.)

The point of the scene apparently though is simply to show that Deep Throat, like the Smoking Man, is an important figure at the FBI as well as in the "defence establishment". The assumption always seems to be that they belong to the "executive branch", which for some reason in the X-Files universe is far more influential than it is in real life, so presumably these people have enough clout with the Clintons and/or Janet Reno to be able to do and get effectively whatever they want. (According to X in 'Ascension', 'They have something on everyone, Mr Mulder. The question is when they'll use it.')

Of course in 'Fallen Angel' Mulder is to all extents and purposes working as Deep Throat's secret agent, spying for Pakula personally on an MJ12 UFO salvage and containment operation. We learn later on that the Syndicate have done a secret deal with the colonists, but the rest of the MJ12's policy is still to shoot first and ask questions later. So this may well be Deep Throat's cover plan if and when he gets found out by the Smoking Man - to claim that Mulder is his asset rather than vice versa.

The first real suggestion that Deep Throat himself is giving Mulder the runaround though (after a certain amount of unsubtle, dramatically ironic foreshadowing) comes in 'E.B.E.' Deep Throat is giving Mulder the truth in this story, but he's also giving him lies. Is he misdirecting him from time to time in order to protect him - because he claims that he's protecting Mulder from truths that (by inference) Mulder is not ready to know? Possibly! But he also tells Mulder that "they" are closely observing him electronically and can "still hear" him. The suggestion then, presumably, is that when Deep Throat says he lied to Mulder to protect him from "the truth", the real truth that he's trying to protect Mulder from is that he suspects that he, Deep Throat, has been rumbled, and so he is now bluffing his colleagues by openly (i.e. in Mulder's apartment) handing Mulder disinformation. Whichever way one slices it though, the point of the story is that by this point Deep Throat has got cold feet and therefore to some extent is prepared to help his military colleagues mislead Mulder. (And arguably this allows him to save Mulder's own arse at the end of the episode when - yet again, implicitly - his colleagues trust him enough to apprehend Mulder and then let him go again.) By the end, however, Mulder doesn't know which lie to believe, however much he wants to.

One subject about which Deep Throat may be telling the truth, on the other hand, is what is later referred to (in the Smoking Man's apocryphal 'Musings', that is†) as UNSCR 1013:

After the Roswell incident in 1947, even at the brink of the Cold War, there was an ultrasecret conference attended by the United States, the Soviet Union, the People’s Republic of China, Britain, both Germanies, France and it was agreed that should any Extraterrestrial Biological Entity survive a crash, the country that held that being would be responsible for its extermination.

Conspicuously missing from this little list of countries are the three "former Axis" nations represented by the officials who end up calling the CSM (and by implication Garnet) in 'Anasazi', specifically Italy, Japan and (presumably, rather than Germany!) Austria. In '731' we learn that the Japanese government is prepared to do a deal with Dr Shiro Zama to take on his still living human-alien hybrid (and, presumably, sponsor his research). So one can speculate that the reason these governments are interested in the MJ12 files is that unlike the goody-two-shoes UNSC permanent member nations they are still officially open to the possibility of doing deals with extraterrestrials. (Have they even, albeit unwittingly, been sponsoring the Syndicate from afar?)

The next time we see the CSM, in 'Tooms', he seems to have graduated up the food chain from Section Chief Blevins's desk to that of Assistant Director Walter Skinner. It's confirmed that, unlike Mulder's superiors at the FBI, the CSM's concern with the X-Files is not that he thinks they're a waste of time and money but that Mulder may be too good at what he does - getting near the truth.

It's only in the very last episode of the first season though that we really get the first incontrovertible hints that there's more to "Government denies knowledge" than just the MJ12. For the first time it is implied that the Smoking Man is both of the Government and yet somehow not of it, and that within the official Government's official cover-up "conspiracy" there is another conspiracy even more ruthless, with its own even darker purposes. Deep Throat seems to imply that Dr Berube's experiments in human-alien hybridization are being shut down simply because they got out of hand - they were "too successful", and when one of the test subjects not only survived the experiments but was found to be running around outside alive and well, it was time for the military in "Los Alamos" to bring them to an end. But he also talks about 'so-called "black organizations"' and '[g]roups within groups ['[i]nside the intelligence community'] conducting covert activities, unknown at the highest levels of power'. In other words, this is the Syndicate in all but name. He seems to be trying to suggest that he doesn't really know about the actual Syndicate, though we can guess from what we find out in later episodes that he is quite probably a member. (Presumably he wouldn't want Mulder to associate him with them too closely when the latter does eventually find out about them. And of course it's also possible that Deep Throat knows or suspects that the real reason that Purity Control is being shut down is to stop the Colonists from finding out its real purpose - i.e. following on from his old friend "Bill Mulder's project" - to find a vaccine for the Black Oil. Perhaps it's for Bill's sake that he doesn't tell Fox any of this just yet - and of course he'll never get the chance to later!)

Indeed several things point to this being an operation by what we will later come to know as the Syndicate:

1. we will later discover that although the 'Purity Control' experiments probably were originally about creating super-soldiers for the military, after 1973 they came to be about: (i) creating the means to turn the Syndicate (and their families) into human-alien hybrids so that when alien colonization begins they will be immune to the Black Oil (aka Purity) and thus survive the colonization process (and not have monsters jumping out of their tummies), whilst at the same time "hiding in plain sight" (from their fellow humans, especially any who've survived without being stung into becoming hosts for alien foetuses) in order to serve as a "Vichy Government" for the invading extraterrestrials; and/or (ii) creating a vaccine for the Black Oil that will allow them and the human race generally to resist the colonization process;
2. we will also later discover that cover-ups of this sort, both for "the Government" and for the Syndicate, are almost always delegated to CSM's group Garnet, so the Crew Cut Man and his and his fellow nameless "men in black" goons are almost certainly working for Busch††;
3. Deep Throat's little speech to Scully just before he dies about 'That's the kind of people you're dealing with!' suggests (as does his dying 'Trust no one.') that there's more going on here than just "Government" secrets - because these are the sorts of people who would happily betray the US government in order to save their own skins; and
4. fourthly, it's not explained why the alien foetus that Scully manages to abscond with from Fort Marlene then ends up in the CSM's Pentagon storage facility.

On this last point, it's just possible that what we're seeing here in 'The Erlenmeyer Flask' is the first real evidence that although the CSM has a cushty billet at the Pentagon and although he and Deep Throat have various mysterious ways and means of pulling strings both in the military and at the FBI, the two of them have actually been loyal to their own "government within a government". In closing down Dr Berube's experiments and bumping off a man who by leaking to Mulder (whether it was misinformation or the truth!) had become a liability, it's the Smoking Man's people who have ended up getting their hands on '[t]he wellspring ... the original tissue'. Although in 'One Son' it's slightly retconned (because apparently the alien foetus did end up back at Fort Marlene), the final scene, mirroring as it does not just the final scene of the pilot episode but also that of Raiders of the Lost Ark, leaves hanging a very heavy inference that the Cigarette Smoking Man is someone we will see again.

*In 'Young at Heart' Deep Throat talks about "the Government" being interested in the dodgy doctor's research, and Mulder, who has never seen him before, speculates that the CSM is from the CIA. But the fact that both of them are interested in the case, and the perfectly reasonable suggestion some have made that the military might want the secret of youth for their super-soldier project, would suggest that "the Government" even in this episode means the Pentagon. (OTOH we also learn, albeit from the man himself in 'E.B.E.', that Deep Throat is ex-CIA - and we know from JFK that you never really leave "the Agency".)
†In real life UNSCR 1013 is a fairly boring resolution passed in 1995 about arms flows in Rwanda.
††The CSM is clearly the head of Garnet, but as such he evidently has two "hats": sometimes, when working directly for the MJ12, he can call upon military personnel (such as as in 'Anasazi', when he's trying to recover the stolen MJ12 files, and in 'Apocrypha', when he's moving a UFO that's mentioned in the MJ12 files); otherwise, he uses his own MIBs such as Krycek and Luis Cardinal, who are (supposed to be) loyal directly to him.