The X-Files: The Shape of the Conspiracy - Part Two: Kidnapping and Clones

Herrenvolk

As in the good old days when the previous Doctor Who's outgoing script editor would write the first serial of any new Doctor, 'Little Green Men' feels like a season one story meant to refresh our memories. It makes little sense, beyond that the military are still the bad guys and the Smoking Man is pressuring Skinner to close down Mulder's work. Sen Richard Matheson is presumably the connection in Congress that Mulder mentioned in the pilot episode. But here he functions mainly as Deep Throat's replacement. The only real revelation of the episode is Skinner, who now suddenly starts to come into his own, apparently protecting Mulder by keeping him in an inconspicuous job, albeit one that's well beneath his talents and dignity. (Later on, in 'Ascension', he says 'I can't protect you, Agent Mulder.' The clear inference is that he has been protecting Mulder so far.) And the 'Get out!' scene with the CSM is priceless.

Skinner comes even more into his own in the next episode, in which we learn that he's basically been trying to restart the X-Files by the back door. His 'This should have been an X-File!' is one of the most haunting lines of the entire show. (At least it was for me.) And when he does eventually reopen the X-Files in 'Ascension', because 'that's what they fear the most', it's something of a spine-tingling and/or punch-the-air moment. In fact all things considered 'The Host' is a really good reboot episode for the series as a whole. (On a personal note, it was the first full episode I ever watched, back in the day, on dear old Auntie's very much terrestrial second channel, and it immediately cemented the show in my family's weekly telly schedule.) Yes, the story is crap, but it's literally so - and that's a good thing! And yes, there's something glorious about the fact that Darin Morgan, who would go on to become something of a guru for those who like the "monster-of-the-week" episodes, started out playing an actual monster-of-the-week in that cheesy "fluke man" costume. Of course as yet there's still no real difference between the two types of episode, and in retrospect that's actually a very pleasing thing.

'X', like Deep Throat, is a spy from inside the military. This is all but confirmed later on in 'Fresh Bones'. (More specifically, he's probably ex-Marines.) Currently though, he's "at the FBI". (It's a normal enough career path, after all.) In 'One Breath' X has a little rant at Mulder in which interestingly he reasserts the conditions that Mulder and his "predecessor" worked under. 'You’re my tool, you understand? I come to you when I need you.' But it's quite a different relationship. 'I don't want to be here.' he barks, in 'Sleepless'. Are we still supposed to believe that he, like Deep Throat, just wants to use Mulder for the same ends (i.e. to expose the fucked-up shit the Government is getting up to with aliens and alien spaceships and alien gene therapy and, er, getting loonies who've been interfered with by aliens to kidnap sexy FBI Agents and hand them over to the Navy for Japanese scientists to do, er, weird things to them)? Presumably! But we feel that X's motives are personal rather than political. He's loyal, albeit in a somewhat grudging way, to his "predecessor" Deep Throat and to Deep Throat's ideals. But we never really find out what the connexion was between them. Given their quite different characters one can theorise that the nature of X's "loyalty" is one of personal honour rather than shared sentiment. (Did Deep Throat save X's ass in 'Nam? It's possible. X looks old enough.) Whereas Deep Throat claimed he was trying to make amends for his sins, we feel that X has been hurt by the system and wants revenge on it. And whereas Deep Throat always came across as a patriotic patrician ashamed of what his country had become, who was seeking to expose a nefarious conspiracy even at the cost of his own life, X has more of an angry black radical vibe. (Even X's disdain for opera in 'End Game' hints at a man who fundamentally despises the Establishment and wants to survive long enough to dance on its grave.) In 'Soft Light', when X effectively manipulates Mulder into leading him to Dr Banton, we get our first, er, glimmer of how he might be using Mulder: just as the Smoking Man used Mulder and Scully to retrieve Ray Soames's tracking device and the alien foetus from Fort Marlene, so presumably Deep Throat could always claim as cover that he was running Mulder as his own double agent within the Bureau. But in truth this is almost certainly just X at the same stage as Deep Throat was at in 'E.B.E.' - abusing Mulder's trust (not to mention sacrificing various mostly innocent lives along the way) out of fear that his own credit with the Syndicate may be about to run out.

The real watershed episode is of course 'Duane Barry', in which we "learn" (for want of a better word) that "the Government" are "in on it"

DUANE BARRY: The government knows about it, you know. They're even in on it sometimes. Right there in the room when they come. They work together with a, uh, secret, uh, corporation. ... A man, the military. They're all in it together. ... The government knows why they're here, but they wouldn't dare let the truth out. So they cooperate.

I have to say, personally, that I've always thought the new idea of the dear old, sinister old "Government" co-operating with extraterrestrials to be something of a lapse in tone for the series. Frankly, men in suits may be scary to crazy hipster libertarian types. But for me the vision of the men with the goofy tie-pins standing next to the creepy child-aliens just made the latter seem considerably less creepy. And fundamentally the whole idea of men dressed as bank managers nattering away to little green men is frankly just silly. It's a concept that gets somewhat salvaged later on, with the whole idea of the conspiracy within the world's governments working in secret to become the Vichy Government to the Alien Colonists' invaders, along with slogans like 'Resist or serve' and 'Survival is the ultimate ideology'. But at this point the revelation comes as something of a "now you're being silly" moment.

And then again, the whole idea that it's not really the government but a "government within the government", made up of men wearing stripey shirts and stripy ties, is itself somewhat disappointing - as indeed, for that matter, are the "politics" of The X-Files generally. But I digress.

Ostensibly at this point, the Smoking Man and indeed Alex Krycek are still just secret agents for the military, acting in secret for the sake of national security. (For all his pixie good looks, we can easily imagine that Krycek is ex-military as well. We later find out that he's a Russian secret agent, but hey, these things happen.) But the extreme possibility is dangled out for us not only that they look down on FBI dogsbodies like Skinner but also that they have no real loyalty either to the military, whose alien foetus they didn't return at the end of 'The Erlenmeyer Flask' or, indeed, to any legitimate government. And if they're the ones behind Scully's abduction, and in other words if they're controlling Duane Barry, then they may as well be the "secret corporation" that's "cooperating" with "them".

We later find out, in 'Anasazi', that the Smoking Man's "day job" is as head of Garnet, and it's the nearest we ever come to discerning what his actual official position is in the whole US (and international) establishment. Indeed it's almost the only time we see him actually break sweat over a case. As the MJ-12's chief troubleshooter he's essential not just to the generals who are trying to keep the truth about UFOs out of the limelight but also to the Syndicate itself. More generally, it's given him carte blanche, in the name of national security, so glide around not just the J. Edgar Hoover Building and the Pentagon but pretty much everywhere, keeping an eye on government secrets and finally, apparently, building up literally a vast storeroom of his own. And he's been around for so long that in the upper echelons of the FBI they can no longer even remember his name.

In 'Ascension' he gives Krycek some blather about not killing Mulder for fear of 'turning one man's religion into a crusade'. It's a cute line, and indeed it's repeated again and again in later episodes. (He uses it to Bill Mulder in 'Ansazi' and to Strughold in the 1998 movie, and clearly he's used it so much by 'Talitha Cumi' that even X has heard it.) But it's not terribly satisfactory, and one cannot blame the writers for retconning later on that the real reason he doesn't want to kill him is that the Smoking Man actually admires Mulder. (A mere two episodes later he tells Mulder to his face that he likes him, and we later find out, of course, that he's Mulder's father. In 'The Erlenmeyer Flask', Mulder refers to Deep Throat as Obi Wan-Kenobi: perhaps it was inevitable that the CSM would turn out to be Darth Vader.) It's just possible that even in the early years the Smoking Man was grooming Mulder as a possible ally in case things went pear-shaped with the Conspiracy.

Mulder for some reason (though we later find out he was right) assumes that Scully was abducted by the Navy, presumably on the basis that he knows he didn't kill Duane Barry so the Navy must have covered up his cause of death. (And Mulder calls Krycek 'Alex'. Soooooo cute! Ahem!) Yes, this feels like another lapse of judgement. The Smoking Man can sit in on meetings at the FBI, and he's got a big private stash of alien gizmos at the Pentagon. And somehow he also has a hold over Krycek, Blevins and, to a lesser extent, Skinner. (And no, we never find out how, exactly! For some reason we're just supposed to picture him as some sort of school superintendent, who can make people sit up straight and look nervous whenever he's around. "SKIN-ner!") We're encouraged to imagine (from the final scene of 'The Erlenmeyer Flask') that he's from "the executive branch", but what does that mean exactly? That he plays golf with the President and can have anyone who works for any government agency immediately fired on a whim. (According to X, referring to Sen Matheson in 'Ascension', 'They have something on everyone.') Or are we supposed to accept that anyone who knows anything about him knows the deep dark gangster secret of state power, and that none of them wants to end up like Deep Throat? It's fine, on a level of immediate drama - tone and setting and so on. But given that just two episodes on from 'Ascension' we find out that he's just a lonely old man who lives in a dinghy apartment, as X-Files mysteries go it's even less satisfying than most.) The only, slightest hint of an explanation we ever get is that as head of Garnet he has the authority of some sort of permanent executive branch, inter-agency chief "fixer". But is it really feasible to imagine that he has the entire US Navy at his beck and call?

Well anyway, for some reason the Navy kidnap Scully, they access her medical records by using a weird genetic tracking device that was put in her arm when she had her smallpox jabs, they snaffle her ovaries to make baby alien hybrids (albeit still quite crap ones that don't last very long), they put a Japanese microchip in the back of her neck to stop her getting cancer (and possibly to read her mind, possibly even to call her back whenever they feel like it using some hokey alien mind-control device!), and then they dump her back at the Georgetown Medical Centre. It's not at all clear how this all came about, but we're invited to believe that this is all part of a long-standing secret tri-services alien hybridisation programme. (Still all sold to the military as being in order to breed super-soldiers? And covered up in the name of "national security"? Presumably!) So presumably the Smoking Man just got her name on the list. And got them to accept deliverance at a UFO abduction hot-spot! From a gibbering loony in drawstring pants called Duane Barry!

And, er, then she got lost in the bureaucracy and ended up half-dead and half-alive at the hospital attached to her old uni in Washington. Because, er, these things happen! It is of course quite plausible that some sweet old navy doctor recognised Scully from some Christmas party when she was a kid and so quietly had her dropped her off at Georgetown. This would at least explain why the Syndicate, presumably smarting because they never got a sample of Scully's blood, dispense one of their thugs to pick one up from the hospital.

Of course, the Smoking Man claims that he was responsible for returning Scully because "he likes her", but it doesn't quite ring true - or at least not quite so true as his "I like you" to Mulder (because, er, I am your father, ahem!). His 'I'm in the game because I believe what I'm doing is right' though does have a glimmer of plausibility. It's possible that even at this point Carter was imagining the great project of the conspiracy - to resist colonisation or to serve the colonists, and to make sure their families (in C.G.B. Spender's case his wife Cassandra, and maybe one or other of his two sons Jeffrey and Fox) would survive. Certainly the 'If people were to know the things I know, it would all fall apart.' is a meme that's going to come up again and again before the conspiracy arc is exhausted. (And yes, the 'This'll be our secret.' is fabulously pedo.)

There's a sense in which 'Red Museum' is a sort of last hurrah for early-style X-Files. I starts out "monster of the week" and, after a fabulously overstocked* set-up (not just handsome teens being abducted at night and ending up in the woods in their underpants, but loads of paranoia - i.e. paranoia about eating meat, paranoia about vegetarian New Age cults, paranoia about teenage violence and rape, paranoia about modern farming methods, paranoia about peeping Toms and pedos, paranoia about family doctors, paediatric medicine and vaccinations, paranoia about, er, the government... and, of course, paranoia about paranoia) suddenly who should emerge out of nowhere but the Crew Cut Man (who killed Deep Throat)? Yes, by inference he's still working for the Smoking Man, so the experiment he's closing down here is either another hybrid operation (injecting children with alien DNA) or (just as likely!) the flip-side "Purity Control" experiment - "control" meaning probably not so much a 'control' as in an experiment as a means of fighting the spread of the alien virus by creating a vaccine for it. (And are we supposed to imagine that, like Michaud in the movie later on, he sacrifices his life for the project partly because he's been told that he'll come back as a super-soldier?) And of course it's all rounded off, once again, with Gillian Anderson's beautiful sexy vowel sounds and the beautiful chilling finale that the case is still open.

'Colony' of course introduces the theme of alien colonization. (Duh!) In the process, of course, we also get clones, alien viruses and, of course, the Alien Bounty Hunters (and, perhaps more importantly, their race) into the bargain. But Carter's original conception of his great arc seems to have been quite different. According to the original plan, apparently, the "aliens" actually doing the "colonizing" were themselves clones. That is to say (implicitly) that they reproduced asexually. They presumably had some rudimentary "shape-shifting" ability, so that they could look like humans (because by any stretch of the imagination it seems far fetched that an alien race would all look like humans with matching male pattern baldness), but at the same time, irrespective of external appearances, they could also always recognize other aliens. But they had no real individuality. (We learn later on that the Samantha clones have an "original", archetypal clone, who, if she survives, will somehow ensure the survival of her race as a whole. And the Alien Bounty Hunter's question "Where is he?" in retrospect sounds as if he was referring to an original Gregor archetype rather than simply to the next Gregor on his list.) The reason why the clones are interested in the "government"/military's hybridization experiments (which apparently go back to the 1940s) is 'to erase that aspect which has forced the community [i.e. the colony] to scatter... [i.e.] their identical natures'. If they don't all look the same then it won't look weird if they live together. But alas, they're now being closed down, and this time it's by their own people rather than by the US government. Though the extraterrestrial politics of The X-Files are never really explained, clearly there are nasty right-wingers out there just as there are down here. This at least seems to be the implication of the Samantha clone's explanation that 'The experiments weren't sanctioned. It was considered a dilution of their species, a pollution of their race. So a bounty hunter was dispatched to destroy them and terminate [Terminator-style] the colony.' The Bounty Hunters apparently are chauvinists who take the concept of "identity" very seriously. (One idea from this early stage that certainly didn't survive was that of the "impure" Gregor clones' wanting "to share the planet" with the "pure" Bounty Hunters. It's barely audible in the screened version of 'Colony', but just about detectable if you put on the subtitles.)

In practice, even Mulder doesn't quite believe this shtick from Samantha about racial purity. But at the same time there's a certain thematic elegance to all this, so it's something of a pity that so much of it was later implicitly jettisoned and retconned out of existence. The only thing that doesn't quite sound right, oddly enough, is the Samantha clone's claim that there were two clones who originally came to Earth in the 1940s and pretended to be her parents. If they really had arrived in the 1940s, presumably they would have been so old that they could only have posed as her grandparents. And since the only clones we see who are old enough to have been born in the 1940s are the Gregor clones we must, alas, admit that the story about the two original parent clones was probably a fib. After all, since when did clones need more than one parent, especially if we're supposed to imagine that like the hybrids in their vats in 'The Erlenmeyer Flask', clones can be grown to term in giant fish tanks?†

One of The X-Files's great strengths of course has always been that, unlike every other show on American TV (though not unlike older British shows such as Doctor Who, of course!) it never had a "bible": scriptural authority was never an issue, and sometimes even the show's fundamental doctrines could evolve and change from one season to the next. In the case of the hybridization and cloning experiments, it's not long before the show is using the two words interchangeably. (In 'Memento Mori' Mulder addresses the Kurt Crawford clones with a cheery 'You're hybrids!' and they don't disillusion him. And in the movie the Well-Manicured Man says 'Without a vaccination, the only true survivors of the viral holocaust will be those immune to it - human alien clones.') And yes, unlike the Jeremiah Smiths (who work for the Social Security Administration rather than in abortion clinics, albeit arguably no less improbably) and (we later learn) the Bounty Hunters, the Gregors never "shape-shift", so with a bit of retconning we might just about be able to shoehorn the Gregors into being not alien clones but human clones whose genes have been spliced with alien DNA. And arguably we can legitimately speculate about the nature of the Gregors' attempt to erase their identical natures, and about the individuality (or "freedom") that they were hoping to achieve for themselves: the only reason the extraterrestrial colonists would have engaged the services of a bounty hunter must have been that the Gregors, via their hybridization, had discovered a way to resist the Black Oil. We learn later on in 'The Red and the Black' that the Alien Bounty Hunters' race have started their own resistance movement against the Colonists, but these clones are evidently the original "rebel colonists". (Their goal of subverting "the Project" is shared by the Kurt Crawford clones in 'Memento Mori', and indeed we are probably supposed to imagine them sharing a similar grisly, bubbly green fate.) But then how things changed from season to season! In 'Colony' the Alien Bounty Hunter arrives from outer space in a UFO. In 'Talitha Cumi' he's apparently just bumming around New England waiting for a call. And by 'Memento Mori' these things can apparently be left to the Grey-Haired Man - who, despite not being very nice, is apparently quite human.

The Gregors' relationship with the later X-Files mythology (not to mention the later X-Files clones) does of course raise the whole question of timelines. We can legitimately deduce that there have been three periods when batches of the clones that appear in The X-Files have been produced: the original Gregor clones were apparently "born" in the 1940s, the first batch of Adam and Eve clones and the Samantha clones that appear in 'End Game' (and presumably the Kurt Crawford clones that appear in 'Memento Mori') were cloned in the 1960s, and the cute little Samantha and Kurt Crawford "drone" clones were products of the 1980s. (And finally, is William a clone as well? Was there one final batch of millennial-baby clones? It seems we'll never know, but the final shot of 'My Struggle IV' would seem to suggest that William has the standard "hybrid" abilities of surviving gunshot wounds and breathing underwater that were established in 'The Erlenmeyer Flask'.)

So was Samantha cloned when she was born? If she was, we might imagine it was her father's doing. Was the original Samantha a test-tube baby? Was Bill Mulder himself unable to get children naturally? It would certainly cast both his relationship with his divorced wife and his wife's affair with the Smoking Man in a different light. And did he put Samantha forward for the cloning programme because, you never know, a spare favourite child might just come in handy one day - not that such a plan would have worked, of course, because presumably the aliens would have "just known". But having his own daughter cloned, before later getting in touch with the Gregor clones from Russia, could well have been an early gesture of defiance, showing faith in the cloning programme and a personal commitment to the survival of his genetic inheritance. It also seems possible, if Samantha was that important, that that was why the Smoking Man was keen to hold on to her, as we later learn he did in 'Closure'.

The question then of course is why? What was the point of making all these clones? We learn from Chris Carter's "secret track" that the "Purity Control" project began as a series of cloning operations in the 1940s, 'its original conception the brainchild of German scientists given immunity themselves for war crimes, and allowed to continue the eugenic experiments that were Hitler's dark legacy.' It's perfectly possible that Carter was thinking of The Boys from Brazil at this point, and we know from 'Eve' that the US military were initially interested in clones for their super-soldier project, so it's quite possible that that's how the conspiracy started, well before the start of the hybridisation experiments and long before the great betrayal of 1973. (Of course it's also possible that by this stage Carter is confusing 'clones' and 'hybrids' willy-nilly.) And even when said "Nazi scientists" started splicing human DNA with alien it's perfectly plausible that the "control" in 'Purity Control' meant just that - because what better control group could one ask for than one made up of clones?

We can take it for granted that the Samantha clones tell Mulder that his sister is alive because they are manipulating him. (Somewhat cruelly, it has to be said - but, then again, survival!) But why does the Bounty Hunter then confirm it? Quite honestly, that's a tough one. It is just possible that he knows about the "walk-ins" who took her in 'Closure' - though again, in The X-Files we're not really supposed to know what happens "off-world". (As it happens, Cassandra Spender confirms in 'Two Fathers' that Samantha is 'Out there, with them. The aliens' - though admittedly this was more than a year before 'Closure'.) It's also possible that there are now so many Samantha clones knocking around that no one can remember which one is the real one - except the original one presumably, which could have been a neat Twilight Zone-type story to tease out, if anyone could have been bothered. Finally, in all probability the Bounty Hunter has just got it wrong. He was privy to the original abduction (because according to 'Within', abductions is one the services the Bounty Hunters offer) but not to the decision to return her just a couple of years later. If this is the case, it casts an interesting light on the whole galactic economy. The Bounty Hunters aren't controlled by the Black Oil. They do what they do because (by definition!) they're paid to by the Colonists. But how? With what? One possibility that springs to mind is that the Bounty Hunters really love their whole sweet, sweet shape-shifting gig and basically are just junkies for the DNA of different species, so the Colonists supply them with the means to travel between planets on condition that some of their best soldiers and assassins do a few jobs for them in return. (It's not so far-fetched when you consider that one of Carter's main inspirations for the clone/hybrid episodes is the old 1960s TV-show The Invaders.) The Colonists themselves, it later transpires, are actually quite slight, gentle creatures - albeit amoral, and with little more than disdain for humanity.

We might even speculate, given that we later learn that it was not the Syndicate but the Russians who eventually managed to develop an antidote to the Black Oil, that the Gregors really are from Russia and that their operation was the true beginning of "the resistance". And if the cloning of Samantha really was part of a plan by her father then it might well explain why he's oddly quiet in the 'Colony'/'End Game' story. If he's in on the Gregors' and Samanthas' resistance plans, his sitting outside smoking when Fox arrives at the Vineyard is lest any interaction between him and the clone give the game away to his estranged wife. It's also possible that his claim that Fox's mother wanted him to come is a fib. (Actually it was he.) And it would explain his reaction - frustration and anger, and an oddly faux concern for his estranged wife's feelings rather than personal grief -  when he learns that Mulder has "lost her" again. Certainly we later learn that he's on the Syndicate's "resistance" wing. (Indeed, in 1973 he was the lone dissenter in the vote to cooperate with the Colonists.) And so of course the reason the Bounty Hunter is there to terminate the Gregors and Samanthas is because (so far) they're the most dangerous potential resistance to the project that the colonists have yet come across.

And of course all this means nothing to the military - the best reason yet to think the the Syndicate's deal with the aliens (handing over their children as hostages in return for baby aliens to do experiments on, on condition that they produce a hybridization process that will allow them and their children to survive the Black Oil's colonization process so that they can act as a "Vichy Government" for the colonists, etc. etc.) is unknown to the wider US "government".

Alas, that would change quite drastically as the whole politics of The X-Files became re-imagined at the beginning of the Season Three.

*No pun intended!
†Incidentally, there's a weird sort of superstition amongst fans either that the alien foetus in 'The Erlenmeyer Flask' cannot be a true alien (because of the first movie) or that the aliens can reproduce sexually (despite the movie). In reality, there's no reason to imagine that the aliens gestate in any way other than as we see on screen: the Syndicate's bees are intended to infect the human population with the Black Oil, who will then be impregnated with alien foetuses that will come to term as violent, heavily clawed and armoured monsters. Presumably the hybridized members of the Syndicate would then have the job of taming them and helping them to mutate into their final "Grey" forms. (Again, this isn't just from Alien(s): it's also largely inspired by The Invaders. Alas, it's an idea that was ultimately missing from Prometheus/Alien: Covenant that the human race was in fact originally engineered to act as a host race for the xenomorphs, the Engineers' plan being first to "seed" Earth with their own DNA, and then to "seed" the human race with their X Files-style black goo in order to produce a new third race of purest malevolence. Indeed, The X-Files started as a clone of Twin Peaks, but it soon became a hybrid of every science-fiction film and TV-show you can think of. A bit of reverse genetic engineering was only a matter of time.)

Theories about The Prisoner: Drama vs. Allegory

Why did No 6 resign?

• He found out about the Village, or at least that he was working for the sorts of people who ran the Village. He perceived either that the British secret state - perhaps even the entire British Establishment itself - had become so morally decadent (or had been so subverted) that it was no longer behaving constitutionally. It may even have been infiltrated by a malign agency or agencies unknown. In any event, No 6 felt in conscience he could no longer work for these despotic and amoral "new masters" (quite possibly some sort of X-Files-type shadowy one-world government sort of conspiracy!), so he resigned.
• He did not necessarily know about the Village, but he knew what sorts of things were going on there.
• It's possible that he did already know about the Village in principle, possibly even because he helped to devise it, only late finding out how his plan was actually being implemented - or perhaps, rather, abused.
• He found out that he was No 1 - or at least that his superiors were doing what they were doing at least partly in his name as Britain's number one spy. He no longer wanted to be a leading light in such operations.
• He may even have resigned in the hope of avoiding being sent to the Village (or somewhere like it) himself - though he would probably have been aware of what a vain hope this was. During the scene of his actual abduction, there is more than a hint of Stoic resignation in those blue eyes as he realises he's being gassed. Besides, his "beach holiday" doesn't seem like the sort of holiday he would really have enjoyed (being more of a skiing man), so it's possible that he didn't actually expect to get that far - though it's also possible that the beach holiday really was just an old professional cover he intended to use. (He doesn't actually deny the possibility in A.B.C., merely that he did not intend to "sell out".)
• Patrick McGoohan resigned - from Danger Man. Lew Grade asked him why. Though McGoohan never seems to have said so in so many words, clearly Danger Man was for him too idealised a version of the morally questionable reality of covert surveillance, subversion and guerrilla warfare that all modern governments perpetrate, both internationally and domestically!

Why do the No 2s keep asking No 6 why he resigned?

The original purpose of the Village was simply to protect the data of retired secret agents. If they just wanted to prevent No 6's information from falling into the wrong hands though, the No 2s would simply have killed him, but they didn't. They want to extract the information he has first. In order to do this they will destroy his individuality if necessary (or perhaps even if it's not necessary). In the "allegory" of The Prisoner, according to McGoohan, this was the actual point of the Village - to destroy the individual.

• At first the No 2s think No 6 resigned because he discovered something valuable and they want to know what that was. 
• Later on it becomes clear (e.g. in 'The Chimes of Big Ben') that they hope that if he answers just one simple question (i.e. about his resignation) he'll crack and tell them everything else he knows as well.
• It's also possible that they suspect and fear that he has discovered too much about their own operations - perhaps even the identity of No 1 himself.
• The No 2s themselves almost certainly don't know who No 1 is. This can perhaps be inferred from the evasive answers that many No 2s give about No 1. It is also stated implicitly in 'Hammer into Anvil' and explicitly in 'Fall Out'. In 'Free For All', when No 6 and No 2 are discussing the consequences of being elected No 2, the older man states, 'Number One will no longer be a mystery to you, if you know what I mean.' This sounds like an implicit admission that he doesn't believe there really is a No 1, except in a philosophical sense (e.g. No 1 is some sort of version of God in the Village's quasi-Masonic cult of "government power" - perhaps even Rover himself, which is not impossible, given that Rover is in one sense the supreme symbol of power in the Village. Indeed, at one point at that story's climax No 2's toughs actually seem to be worshipping Rover in some sort of inner sanctum within the Green Dome). For some of the No 2s then, No 1 is a "noble myth", though it's possible that there are others who know that the idea that No 1 is a noble myth is itself a lie. Some of the No 2s may indeed want to know more, so for some of them breaking No 6 to discover whether he knows who No 1 is - or at least whether he knows more about the Village and the powers behind it than they do - is a matter of personal concern to them, as well as of personal honour.
• It's even possible that some of them know (or suspect) that he is No 1 and wish to break him in order to replace him. (This may actually have happened by the time of 'Do Not Forsake Me Oh My Darling' and apparently has happened by the time of 'Fall Out', in which No 1 seems to be No 6's doppelgänger Curtis.)

Who is No 1?

• The original answer (and the only acceptable answer) to 'Who is No 1?' is of course that No 1 is No 6. He is the most important person in the Village, after all, and certainly its most important prisoner. It's not necessarily clear though whether or not he knows that he is No 1.
• The question is of course No 6's equivalent of 'Why did you resign?', the implication being that if he can get them to answer one of his questions then he will have turned the tables on them decisively. 
• He probably either knows the answer or suspects it even as he's asking the question. The difference though is that the No 2s themselves don't know who No 1 is. Whatever they may suspect, they only know that No 6 is important, not that he is No 1.
• It would be most satisfying to imagine that 'Who is No 1?' and 'Why did you resign?' actually have the same answer. Originally the idea was that No 6 had devised the idea of the Village but then resigned when he discovered how/that his idea had been realised. The Prisoner therefore is No 1 and he resigned because he is No 1 and had a change of heart about the Village and what was being done there - or at least he had a change of heart about his job once he realised the sorts of things that were being done by the people he was working for (i.e. the sorts of things that were going on in the Village). Having been the best agent in the service he became its most implacable opponent.
• If he knows that he is No 1 but knows that they don't know, then the question is really little more than a taunt.
• If he knows that he is No 1 and doesn't know that they don't know, then the question is presumably a genuine attempt to discover if any of them knows that he is.
• It's just possible that despite having resigned he, or rather someone posing as him, is still recognised as No 1; and so, in a classic game of bluff and double bluff, whereas the No 2s' objective is to discover whether he realises this, his intention is to discover how it is that the Village continues to function even though he himself is now a prisoner.
• It's just possible that the impostor who has replaced him as No 1 - the figure unmasked by No 6 in 'Fall Out' - is No 6's doppelgänger Curtis, who was not killed by Rover in 'The Schizoid Man' but only stunned. (Does Rover ever actually kill anyone?) It's also possible that Curtis was revived after 'The Schizoid Man' in much the same way as No 2 is in 'Fall Out'. Despite being brain-damaged by his trauma, he was given No 6/the true No 1's place at the "controls" of the Village.
• Implicitly there's not just a No 1. Above and beyond (or, indeed, below) the Village, there's also a No 0 - who is quite possibly the Butler, who still controls No 6 (but more subtly) even after he has left the Village.
• Another good candidate for No 0 is of course Rover - not just the supreme symbol of power in the Village but also the "reset", who returns escapees and thus returns everything to the status quo ante each time they attempt to escape.

Patrick McGoohan, who plays No 6, came up with the idea of the Village based around Portmeirion, which had been one of the locations for Danger Man. According to McGoohan though, No 1 is No 6's self. By implication then, No 1 = No 6, '1' is 'I' and '6' is 'me': one is the self as seen by oneself (the Prisoner himself) and the other is the self as seen by society (the Village). The Prisoner is his own worst enemy because he constantly "looks out for number one". McGoohan also made the point that you can't rebel against society all the time, otherwise you'd go crazy. So No 6 wants to escape from the Village because he rejects society. (He may even deny that there is such a thing as society.) But, as a member of society (i.e. as a number), he cannot escape it, even if he appears to have escaped and,for a time, to have shrugged off its label.

To a certain extent it's necessary to "retroject" this fable's moral onto some episodes, but it works remarkably well. The Prisoner cannot escape the Village because one cannot escape society, and even if one can escape society one cannot truly achieve the individuality of pure subjectivity without either going mad or accepting, to some extent, that one must also be an object of others' actions, observations and labels. One will always be numbered by other people, and even as oneself one must have a number - even if that number is, indeed, 'One'.

It follows though that in all probability each and every individual is No 1, and that anyone else who pulled off No 1's ape mask would see his own face. In as far as he has objective reality, No 1 is a faceless, protean being who represents the dark, utterly selfish, animal side of each man's nature. He can be unmasked and confronted, but he cannot be caught or restrained, let alone imprioned. It's quite likely that he is in charge not only of the Village but also of the world itself: the Village has its nukes, just as the outside world does. As such it it quite likely that he is the Lord of This World that Christ warns of in the Gospels - the Antichrist, Satan himself.

McGoohan: 'I think progress is the biggest enemy on earth, apart from oneself.' 

...  

Audience member: 'Do you think there's going a strong popular reaction against "progress" in the future?' 

McGoohan: 'No!'

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.