The Project

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Updated: Two Fathers / One Son


This page includes facts, clues and theories from the whole six seasons. From "The Red and the Black" and the movie onwards, we're beginning to get some answers, but I haven't deleted past theories that seem to contradict this view of what is happening. Nothing is certain in the X-Files.



The Consortium

For facts and figures, see the "Them" page in the character section.

How many conspiracies?

Although we now seem to have settled on an over-riding Mytharc, the first few seasons, at least, offered us evidence of a whole lot of different conspiracies.

  • The Consortium No comment. This is covered everywhere else in this section. Redux II suggests that out old friends the Consortium might be called "Roush"

  • The Military Obviously overlaps with the Consortium. CSM can call out a crack team of soldiers when he needs to and hides his evidence in the Pentagon. X is clearly in the same group as CSM yet he is also privy to military secrets. However, the military retrieval team we see in "Fallen Angel," for example, and the military UFO in "Deep Throat" suggest a military agenda that isn't strictly the same as the Consortium's.

    They have no interest in the DNA issue, but only want the technology. Aliens who crash are to hunted down and killed ("Fallen Angel"), not taken for their DNA.

    Interestingly, the General in charge of Area 51 doesn't know "the truth" either. In fact, he thinks that Mulder knows more than he does. Regarding the craft built with UFO technology: "we just fly these birds. They don't tell us what makes them go." He even asks Mulder if aliens really exist.

  • Local Conspiracies Nothing to do with the Consortium but worth including simply as a reminder that, especially in the first season, many of the cover-ups were local in nature. For example, the sheriff in "Jersey Devil" who suppressed evidence as he was scared of frightening off the tourists, or the fathers in the Pilot episode who covered up what was really happening.

  • Anti-Communists? Back in 1952, at the height of the crusade against Communists, the crusaders seem to have been involved in experiments grafting alien (?) things into humans, turning them into killing machines. It seems if at least some of the Project's experiments came out of Cold War politics. Bill Mulder was involved in this particular conspiracy, through his work with the State Department, but there is no sign on CSM, yet, or any of our other old friends. There are, though, Nazi scientists, suggesting that our friends the Consortium grew out of work such as this.

National divisions

Well Manicured Man says that he represents a global Consortium of interests, and CSM, in "One Son", says that the Syndicate is international, forming together expressly to set aside their national loyalties. However there are signs of national divisions.

  • In "Anasazi" we see Italians, Germans and Japanese, and there are presumably representatives of more countries in the group. However, in "EBE" Deep Throat talks about a secret committee in 1947 which was attended by the USA, the Soviet Union, China, France, Britain and both Germanys. This committee agreed that they would kill any alien that landed within their boundaries.

    Are these countries in on the Project? Or are these the countries who agreed to kill an alien, but America and Germany played the others false and joined forces with Italy and Japan and decided not to kill all the aliens?

  • "Piper Maru" shows that the French aren't in on the MJ files. Krycek sold some information from the tape, leading them to look in the ocean for the crashed UFO.

    There is of course the possibility that some French are in on the Consortium and this is another covert French group getting a piece of the action. However, WMM and CSM wonder where "the French" knew where to look. This wording suggests they didn't expect any French person to know this information.

  • Even the Japanese scientist from Operation Paper Clip, who is to be assumed to be right at the heart of the Project, seems to be creating an unauthorised hybrid and taking it back to Japan. ("Nisei" and "731") Much of these episodes can be explained as some sort of rivalry between the Japanese and American contingents within the Consortium.

  • No idea if the Russians are in on the Project or not, but "Tunguska" and "Terma" shows the Russians and Americans engaged in out and out rivalry to discover a cure for the Black Cancer. The Russians get the cure, but sabotage the Consortium's work. Later ("The Red and the Black") Krcyek, presumably working alone, takes the cure to WMM.

    If, as we're supposed to believe, the cure to the black cancer is vital to the survival of the human race, you'd have thought the two countries would be working together, really. (Although, in "Travelers", set in 1952, it seems as if the conspiracy is all to do with Cold War politics. It's not clear who the "enemy" is, when people talk about the need to develop weapons against them, but it's a fair guess that it's the Russians.)

    Unless the Russians and WMM are both secretly working to get the cure in order to oppose the colonists, but are too secret about it, so neither of them realise that the other is doing it for this reason. If that makes sense.... Or maybe the Americans and Russians, while they want to ensure the survival of all the people in their own countries, aren't too bothered if all the people in their old enemy's country dies.

Personal rivalries

Even within the small group of conspirators who meet in their New York gentlemen's club there are rivalries.

  • WMM and CSM never seem to waste an opportunity to score points off each other.

  • In the "Anasazi" trilogy and "Piper Maru" / "Apocrypha" poor CSM gets roundly criticised by everyone for his handling of the events. He also out and out lies to his colleagues about virtually everything.

  • CSM is capable of putting personal interest above the Project. He does this in "Talitha Cumi" when he allows Smith to cure his cancer in return for his freedom. It is also possible that he does this all the time by not killing Mulder, out of loyalty to his old friend or to Mrs Mulder.

  • In "The Red and the Black", WMM and the First Elder disagree on how to act with respect to the colonists and the aliens who oppose it. WMM wants to join the rebels and oppose the colonists. The Elder thinks this would be suicide, and goes behind WMM's back to return the captured rebel to the colonists.

  • WMM ends up going against the others, helping Mulder, and dying for it. (apparently)

Policy differences

Different people in the Consortium disagree on the attitude to the colonists. While the Consortium has been based all along on the principle that the best way to deal with the imminent invasion is to collaborate, working secretly to stall the aliens, and working on a vaccine to the black oil, some have always been more inclined to oppose the colonists openly. Bill Mulder seems to have been one. Recently, WMM has been another, wanting to join the rebel aliens.


Building a better soldier

Medical experiments

This theme crops up again and again, in that the whole aim of the Project seems to be based around genetic engineering and similar experiments. A lot of it is about producing soldiers who are immune to biological weapons while possessing extra strength. Now, we know now that this was done, at least partly, as part of their deal with the colonists, to produce a hybrid immune to the black oil and able to live on as a slave race after the colonisation. However, but there are also signs that these super powers and immunity are being developed for military purposes, whether to be used in a war against an earthly power along the way, or against the colonists themselves, should the Consortium decide to break their alliance and openly resist the aliens.

  • "Eve" tells us about the Lichfield Project, designed to create a race of superhumans. While the resulting Adams and Eves did possess extra strength and intelligence, they were also prone to madness, suicide and murder. If it had worked, would this have been the start of a eugenics program to fill the world with super humans?

    This could perhaps be linked to the main Project. It could be an early experiment in the genetic engineering and cloning experiments we see later Did They discover that genetic engineering worked better with a bit of alien DNA thrown into the mix?

  • In "Young at Heart" They are interested in getting their hands on Dr Ridley's reseach which will reverse the ageing process and enable people to regrow lost limbs.

  • "The Erlenmeyer Flask." People with terminal cancer are submerged in a vat of liquid and end up with super powers, such as being able to stay under water for days, and with their cancer cured. They can also be severely shot and still carry on running, though they're not invincible. However, while "They" are anxious to find out if this process works, they don't want the living and breathing results of the process around to tell tales. This suggests that there is no immediate situation in which these super soldiers are needed.

  • "Sleepless" shows us the effects of an experiment back at the time of the Vietnam war, designed to keep soliders awake 24 hours a day and so increase their effectiveness.

  • "Red Museum" shows us an experiment (using "Purity Control") which makes people apparently immune to disease. It also causes some aggressiveness and personality change. What better qualities to have in a soldier in some future biological war? It's the same stuff as in "The Erlenmeyer Flask", but a simple course of injections rather than a full vat of liquid. The end result isn't nearly as hardy as the green-blooded products of that experiment, but would still be useful in war.

  • In "731", the Red-Haired Man tells Mulder the hybrid has been created as a weapon - a person who is immune to most ordinary weapons. This presuambly means biological weapons. It can seemingly be killed by a bomb.

  • "Tunguska" and "Terma" are about attempts by the Russians and Americans to discover a vaccine for the "Black Cancer." The militia man says that Saddam Hussain used the black cancer as a weapon in the Gulf. This suggests that everyone wants to use this as a weapon, but would prefer it if their own troops had immunity against it first. A weapon against whom? Another human power? Someone from space?

    The Consortium - or WMM, anyway - now has this vaccine. WMM, at least, seems to think that it should be used to make us immune while we join the rebel aliens and go to war against the colonists.

  • In "Travelers", Nazi scientists, and anti-Communist crusaders, surgically graft an alien (?) being into human subjects, thus turning them into a "killing machine". It's spoken of, probably, as a possible weapon to use in the Cold War, though who can tell what other enemies they may want to use it against?

In conclusion, are quite a lot of the Consortium's experiments actually attempts - further attempts - on a similar line to the vaccine against the black oil - ie efforts to find a weapon against the very aliens they have made an alliance with?

However, "Two Fathers" shows us that creating an alien/human hybrid is, in fact, the very job that "they" have been assigned by the aliens, so many of the medical experiments, and abductions, can just be part of that.

Military technology

This seems to be the work of the military (not surprisingly) While they are very prone to acting secretly they don't appear to be part of the mainstream Consortium Project we see later on. The story is usually one of opportunism in which the military step in to use some development someone else has come up with.

  • "Deep Throat" deals with the development of better faster military planes, possibly built using UFO technology. This seems to be more of a military project than a central Consortium one, though it is rather early in the series to tell. Later, in "Fallen Angel," we see military men hunting down the alien who crashed, while apparently wanting to salvage the UFO, presumably to study and copy.

  • "Ghost in the Machine" sees them interested in getting their hands on the artifical intelligence created by Brad Wilcek. He cites Oppenheimer and says how much he fears that his invention will be used as a weapon. Deep Throat knows about this.

  • In "Soft Light", Dr Banton, who has managed to create an instant weapon of destruction in his own shadow, feared that They would come and do a "brain suck" on him to find out about the process and use it as a weapon. At the end we see that his fears were justified. X is in on this.

  • In "Redux" we are told that the entire alien story is nothing more than a cover, hiding the fact that the military is working on technology of its own. As we are told in "Jose Chung", people look closely at a new spy plane, but a UFO sends them panicking and makes sure no-one believes them.

  • "Dreamland II" reveals that even the general in charge of Area 51 doesn't know if UFOs exist. He and his men fly crafts build with anti-gravity devices and all sorts of other futuristic things, but he actually thinks that Mulder must know a whole lot more about whether aliens exist than he does.

Manipulating Minds

  • "Blood" shows us some experiment done by some unknown person or group. It uses subliminal messages and drives people to kill. However, it only seems to work on people who already suffered from phobias.

    "Wetwired" has a very similar experiment, but this time we definitely know that CSM and his friends were behind it. As with so much the Consortium does, it looks as if it is only an experiment - an attempt to find out if a process works so it can be used in the future, when the time comes, rather than yet.

    "Unusual Suspects" goes back to 1989 but has yet another attempt to manipulate the behaviour of the populace. This this it is a gas that induces anxiety and paranoia. It isn't clear to what eventual use this will be put, but the initial tests are to be performed on ordinary people - and stray FBI agents who wander into the wrong place at the wrong time.

    When will the time come? Is this another weapon in Their armoury when the "date" comes round? Will our televisions all start broadcasting subliminal messages telling us to kill each other, so the surplus population is out of the way? Or will they broadcast reassuring messages telling us how happy the new regime will make us?

  • "Jose Chung" suggests that at least some alien encounters are hoaxes perpetuated by the military. In effect, the popular culture is being manipulated into accepting alien abduction as common, when all the time attention is being diverted from what the government is getting up to.

    This is also the message of "Gethsemene" and "Redux" - that the entire alien story is a catalgue of fakes and mind manipulation, to cover more mundane developments. CSM says this is not true, and we are bound to hear more on this particular claim later, or to prove it wrong.

  • In "Talitha Cumi," CSM talks to Smith about how the people are docile and need to be led and given direction by people such as him. He seems to want the people to lose their faith in everything but science. Why? Is this because the revelation of the "truth", when it comes, will then shatter their last belief, leaving them weak and helpless? (We only have to look at Scully to see that, in her eyes, what we suspect to be the "truth" is contary to her science).

"Alien" abductions

Back at the start of season 1 it was all so simple. Greys abducted people in a flash of white light. When it got more complicated....

Alien abduction

Evidence that at least some abductions are alien:

  • The implants of unknown metal inside Duane Barry, plus the tiny holes in his teeth

  • The leviatation effect on Max Fenig. It doesn't seem as if They have mastered this yet.

  • Time distortion. Mulder has found several example of this. When the bright white light came in "EBE" it wasn't like anything Mulder and Scully had seen before, but there was no time distorion. This implies that, while They can fake certain characteristics of alien abduction, some, like time distortion, are beyond them.

  • Symptoms of weightlessness on Ruby Morris in "Conduit."

  • "Fearful Symmetry". If Japanese scientists wanted earth animals there are easier ways to find them than this.

  • Scully's memories in "The Red and the Black", and what we ourselves saw at the end of "Patient X". These were no Japanese scientists or Consortium men. They came from a space ship, and used technology that, as Marita told the Consortium, is not earthly.

  • The space ship in the Antarctic at the end of the movie.

Abduction by humans

  • "Nisei" and "731" is the clearest statement of this type of abduction. In these episodes we learn that so-called alien abductees are actually taken by Japanese scientists and experimented upon on steel tables in a boxcar. As we learn in "Memento Mori" the women abductees are stripped of all their eggs, which are then used to engineer clones.

  • Samantha now seems to have been taken by aliens after all, if we believe CSM. However, it was human politics that led to her abduction, since the Consortium were hand in glove with the colonists at that time.

    A digression: Are Mulder's memories of her abduction at all reliable? They change all the time, suggesting they may be dubious at best, and "Paper Hearts" shows that he realises this. (Although we know really that this is an accident due to poor research by the writers!). As we see in "Jose Chung", false memories can be planted.

    However, in "EBE" we see that They have mastered the bright white odd light effect. If they've mastered levitation then Mulder's memories could be compatible with a very human abduction. They are certainly compatible with an alien abduction done at the bidding of humans.

    Certainly, "Unusual Suspects" shows that Mulder starts imagining aliens, after being sprayed with some paranoia-inducing gas. He underwent regression hypnosis, and then opened the X-Files shortly afterwards. After what he is told in "Redux", he comes to believe that all his memories of Samantha's abduction were implanted in him and weren't true.

  • In "Jose Chung" we see how the military sometimes fakes abductions.

  • If Mulder's right about the files in "Paper Clip" containing the medical records of all the abductees then the Consortium at least has access to the tissue samples of abductees, suggesting they are behind the abductions in some way, or at least in league with the abductors. "Redux" seems to confirm this, with yet more files in the Pentagon.

Tying it together

  • Just because some "alien" abductions are false doesn't mean all are.

  • Even the human abductions utilise alien technology in some way, such as the genetic experiments that the abductees are subjected to. Thus, in a way, these abductions are also alien in a way.

Theories?

The evidence suggests that the at least some aliens are here, abducting people every now and then (such as Max Fenig). At the same time, the Consortium, possibly using alien-supplied technology, are also abducting people to use in their Project. This could be one and the same. "The Red and the Black" suggests that the abductees are taken by aliens, but so many other episodes show Consortium involvement (eg the implant, which is an alien homing device, yet found in the Pentagon in Redux) Maybe some are one; some are the other? Maybe they share the same technology, so whatever it is that the abductees are needed for can be obtained both in a boxcar with Japanese scientists and in an alien spaceship.

CC, in his movie soundtrack message, says that the Consortium was helping the colonists by abducting people to use them for hybridisation. We see in "Two Fathers" that the abducted people are vitally important to the attempts to create an alien/human hybrid - the Consortium's part of the deal with the aliens.

However, we have a problem. In "one Son", we learn that the aliens are the ones who took Cassandra, Samantha, and the others, after the Consortium voluntarily handed them over. However, Samantha has been gone for 25 years, off somwhere with the aliens. Cassandra, however, has been living here on earth, just taken away for short periods every now and then. Also, she's been taken away by aliens, with the full light and levitation effect, but has been experimented on by human doctors, who have turned her into a hybrid. Hm...

Plus, the humans themselves seem to abduct greys, in that they are fond of getting hold of them, taking samples from them and using them in their hybridisation experiments....

See the Aliens page for more information on the various types of aliens and their interaction with humans.


Colonisation

"The date is set", we hear in "Talitha Cumi". For what? Smith calls it "the Process". Mulder suggests it's colonisation, and X doesn't deny it.

This theme is so central to the emerging plot that I really can't go into detail here. I've kept my original theories here for historical reasons, and because I'm loath to delete anything, given the habit this show has of changing all your certainties. If you want the current "truth" on the colonisation (and hybridisation), go to this page instead: the truth

  • In "End Game" the false Samantha tells Mulder how the clones came in the late 40s and are the advance guard of a possible take-over in the future. They believe that we are forfeiting our stewardship of the planet and they will be able to take over. Did they come at Roswell? Deep Throat says the alien tissue has been here since 1947, and CSM says that the whole thing started at Roswell.

  • "Herrenvolk" shows us the farm of clones, cultivating bees and honey from alien crops. Smith says these represent a "new order of species", suggesting that the bounty hunters are doing their own cloning experiments ready to take over.

    The only problem with this is that in "Colony" the Bounty Hunter was apparently sent to kill the colony for diluting the blood. Why then are the shapeshifters themselves creating hybrids? (And they are hybrids. The boys' mothers are the MUFON women and the girls look like Samantha). Maybe the fake Samantha wasn't being entirely honest with Mulder. Maybe she wanted him to believe that her group was the only hybridising experiment going on when it was in fact only one of many. Maybe the problem was that they were hybridising without permission rather than that there were hybridising at all.

So where do the Consortium come in? In "Zero Sum" we are shown that they knew about the bees all along anyway, so were presumably in the know about all this cloning business too.

In "Talitha Cumi", CSM rebukes Smith for rebelling against the project. This could be read as implying that the Consortium have the upper hand in the relationship, but in the same conversation Smith says CSM wants to be a "commandant" when the process begins. This suggests the possibility that CSM and his friends know that the colonists will be taking over soon and can't be resisted, and want to make sure they're on the right side.

Hey! Prophetic or what? I wrote that last bit in June 1997, and now it's confirmed (well, as much as anything is ever confirmed on this show.) This is precisely the message of "The Red and the Black". The colonists are coming, and the Consortium is joining them in order to survive and, presumably, to hatch a deal to salvage what they can when the date comes. However, some of the Consortium, such as WMM, are thinking about how to resist....

Possibilities?

  • Maybe the Consortium have agreed to help the colonists with their own colonisation projects in exchange for alien technology to create a super soldier. ("The Red and the Black" musing: This still could be so. Part of it, anyway. Why do the deal at all with the colonisist unless they're trying to get something other of it? To win time, and spend that time desperately building up their own technology?)

  • Maybe the colonists expect the greys to fight them for the planet and are helping the Consortium prepare the human race to fight the greys. (Post "The Red and the Black" musing: I still like this one, but it seems less likely now.)

  • Maybe the Consortium are playing the colonists false and are desperately trying to build a better soldier so they can use it against the shapeshifters and clones. (Post "The Red and the Black" musing: Yes.... At least, some of them are working on the black cancer thing as a weapon)

And how many of those sound like bad B-movies, when written like this?


Hybridisation

This seems to be done in two main ways:

Test-tube hybrids

These are true hybrids, created (it seems) from fertilising a human egg with something alien.

  • "Memento Mori" shows this. Also the clones in "Herrenvolk"

  • The clones in "Colony" were growing babies in test tubes, vats and bags.

  • "Emily" reveals how eggs are taken from young woman (like the MUFON women in Allentown, and Scully) and are using to create foetuses that a probably hybrid. These are implanted in elderly women who are given hormones to give birth (naturally) to the hybrid babies. Emily obviously must appear normal, since no-one in the hospital noticed her green blood, but started developing a cyst on her neck - a cyst that contained a corrosive green fluid. Without whatever treatment Dr Calderon (also a hybrid himself) was giving her, this stuff spread and killed her.

    (So, why? Are these hybrids essentially unstable, with the human and alien part of their blood warring with each other, and needing a daily injection to keep them in check? Without this daily injection, Emily died. The greeb corrosive fliud was only in evidence once the cyst grew and she started getting sick. And are the tests and treatments she was getting from Dr Calderon designed to tests ways of getting these hybrids to look even more human, without this pesky green blood? Please note that this is all wild speculation.)

Changed humans

We see these more often. These were originally human but have become something else after various medical techniques.

  • "The Erlenmeyer Flask" by which ordinary humans with cancer were emersed in a vat and emerged, eventually, with green blood and super powers. Deep Throat says this was done by giving them a sample taken from the alien foetus Scully found at the end. This looks like a grey alien, as it has a big head and sloping eyes.

    A weaker form of the same process is seen in "Red Museum"

    These hybrids look human but have green blood.

  • The bodies in the boxcar in "Anasazi". The smallpox scars are meant to imply that these were originally human until something was done to them to make them look alien.

    The hybrids don't look human. They have big heads and eyes, and look rather like greys. Why do they look different from the Erlenmeyer Flask hybrids?

  • In the Pilot episode, the boy they exhumed looked human at death but had morphed into something else after death. This isn't explained.

  • The big one: Cassandra Spender. After years of abductions and experiments, Cassandra has now been turned into a fully operational alien/human hybrid, with green blood and fantastic healing abilities. (Compare the Erlenmeyer Flask ones, who still get injured, though not as badly as normal humans.) We are now to believe that all the others we saw were failed efforts, and only Cassanda is truly successful. However, now she's been created, the colonisation will happen. See "the truth" page for more.

Who does the experiments?

  • The rebel clones in "Colony" who are killed for it. (And is this why the morphs in "Emily" killed Dr Calderon, and, maybe, killed Emily? Again, are they disapproving of the government projects that created these hybrids? They do, however, appear to be doing the "project's" work earlier, so who can tell?

  • Operation Paper Clip scientists like Klemper and Dr Ishimaru. They may or may not have their own agenda too, but seem to have been the scientific wing of what CSM calls "Bill Mulder's project.". This also ties in with the fact that Scully remembers the Japanese scientists from her own abduction, and her abduction seems to have resulted in the birth of a hybrid baby.

    According to Deep Throat, these experiments were done using alien tissue recovered in the 40s, but only recently have they had the technology to actually to anything with it. (However, in "one Son" we learn that the tissue was only given, in the form of the alien foetus, in 1973, so what's going on here? Maybe they had some alien tissue, but, until they had the foetal tissue, couldn't actually do any real hybridisation experiments.)

    Nazi scientists are also involved in the experiments in "Travelers".

  • The shapeshifters themselves? ("Herrenvolk")

  • In "Memento Mori", we see the Kurt Crawford clones acting as the laboratory staff building new fully grown clones, but secretly working against the project since they want to save the lives of their "mothers". It never looks as if they are behind the cloning, though, just working in the project.

Whatever the details, though, it now seems as if Consortium doctors have been working for years to create a successful alien-human hybrid. Despite all we've seen in earlier episodes, it's only now, as of "Two Father", that they've been successful. The successful hybrid is none other than Cassandra Spender. Creating the hybrid is the Consortium's assigned job, by the terms of their agreement with the colonisers. They are the create a hybrid, immune to the black oil, who can be employed as slaves by the colonists. Thus, as soon as the colonists find out a successful hybrid has been created, they will know that it's almost time for them to start coming here. In CSM's words, the creation of the hybrid marks "the end."


Why don't They kill Mulder?

Even as early as 1989 before Mulder got interested in aliens, X obviously had his orders that "this man is not to be touched." Why? Okay, we know the main reason is dramatic necessity, but there are also some internal reasons:

Connections in Congress

  • In the Pilot episode, Mulder tells Scully that he's made connections in Congress and these are the "only reason" he's allowed to continue his work

  • In "Tooms", Skinner tells Mulder "This was close. Any closer and a thousand friends in the Capitol won't be able to help you." This shows that his connections in Congress are protecting him but also that they can't protect him indefinately.

  • In "Little Green Men" and "Nisei" we see Senator Matheson, Mulder's friend in Congress. Both times he helps Mulder by giving him information, but we never see him actively protecting Mulder.

  • Not even Matheson can help Mulder in "Ascension." X tells Mulder, "there's nothing the senator can do for you now, not without committing political suicide." Mulder asks if they have something on him. "They have something on everyone," X replies. "The question is when they'll use it."

  • However, in "Terma", Well Manicured Man says that it is beyond his power to call off a Congressional hearing, implying that there are limits to Their power over senators.

In summary, it seems that the Congressional protection is enough to stop Mulder being suppressed illegitimately, However, with something like "Anasazi" when They make sure that Mulder is committing a real discplinary offense, there is no reason to believe that there would be any friends in Congress who would step in to save him.

Being a Martyr

This seems to be the official explanation given by Them.

  • In "Ascension," Krycek asks CSM why, if Mulder's such a threat, he isn't killed. "Kill Mulder and you risk turning one man's religion into a crusade", CSM replies.

  • Deep Throat assures Scully (in "The Erlenmeyer Flask") that Mulder is too high profile to kill.

  • However, in "Talitha Cumi", X tells Mulder that this issue is important enough that They will kill him even if it will make him a martyr. This suggests that this is a real reason, but that there are circumstances in which it will be overridden by other more pressing concerns.

I have to admit that I don't believe this one for a minute. Who are all these people queuing up to join the Crusade? And surely it's within the powers of Them to engineer some sort of "accident" that not even Scully would question.

Keeping an eye on him

Okay, this isn't a reason not to kill him, but it is a reason not to get him thrown out of the FBI. As Deep Throat says to MacGrath in "Fallen Angel", on the whole Mulder's safer in the Bureau than let lose and exposed to the wrong people. "Always keep your friends close, but keep your enemies closer," he says.

Although we don't see it, Mulder and Scully go submit requests for travel expenses (referred to in "Conduit" and "Fallen Angel") so They can always see where Mulder's going, what he's investigating, plus have a nicely packaged report (by Scully) delivered to their desks afterwards. They wouldn't get that if he was freelance.

Bad Luck

There are of course several times when They have tried to kill Mulder and have only failed by chance. Examples include Crewcut Man's attempt to burn him to death in "Red Museum", the truck loads full of gunmen in "Little Green Men," and of course the burning boxcar and the bullet through the window in "Anasazi".

(Personally I like the idea that They are constantly trying to shoot Mulder but keep missing, as he's always stooping to get his gun back from the floor.)

Navajo Memory

In "Paper Clip," Skinner tells CSM that Albert Hosteen and his friends have memorised the digital tape and will reveal the contents if Mulder and Scully are threatened in any way. However, we don't see or hear anything about this protection being cited at any point. It's not even brought up in "Memento Mori," when Skinner should really have done do in order to get the deal he wanted with CSM. Presumably Skinner's latest deal means that the earlier one is no longer valid.

Skinner

From "Little Green Men" onwards, Skinner makes it clear that, while he doesn't endorse some of Mulder's wilder methods, he is on the side of justice above all. Any signs that They are acting against the law, then he'll step in and protect his wayward agent. (Such as when he shouted at CSM to get out in "Little Green Men.") Yes, he shouts at Mulder, but he's not that fond of people who shouldn't shout at Mulder shouting at him.

Maybe this attitude, coupled with the Navajo tape affair, explains why in season 3 They made few attempts to hurt Mulder and Scully, but had a field day beating up Skinner. In both "Piper Maru" and "Avatar," it was Skinner They attacked in order to weaken the X-Files.

Because it's more fun to torment him while he's alive

  • As CSM says in "The Beginning", "You can kill a man, but you can't kill what he stands for... Not unless you first break his spirit. That's a beautiful thing to see."

Importance to the Project

This is a cryptic one, and rather ominous. In "Herrenvolk" CSM says to the Bounty Hunter, "you know how important Agent Mulder is to the equation". Hmm. Will we find out more about this later?

Because they secretly want him to succeed?

My own pet theory is that they just wanted him to nag at them and undermine them, since they were so desperately trying to stall the colonisation and to proceed as slowly as possible with the hybridisation project. Given that Bill Mulder apparently intended Fox to carry on his work, and given that CSM does tell Mulder everything in the end, why on earth didn't they tell him it all before? What's the big secret that he can't find out? Of course, they don't want the world to know, but why not Mulder? The only real logic I can think of is that they just wanted him to keep undermining their work, getting more and more invested in it.

Cigarette Smoking Man's Sentiment

The more I think about it, the more this seems to be the main thing keeping Mulder alive.

  • In "One Breath," CSM says he returned Scully because he likes Mulder, and likes her.

  • In "Anasazi", CSM tells Bill Mulder that he's protected Fox until now. He says it as a rhetorical question, as if he thinks this should be obvious to Bill from the past few years' events.

  • In "Musings" he makes sure his colleagues understand that Mulder is his to worry about.

  • From "Talitha Cumi" onwards we see the extent of CSM's attachment to the Mulders. He is close to Mrs Mulder and certainly saves her life because of this sentiment, despite all his justification of the need to keep Mulder from becoming desperate. Is he Mulder's father or not? For this issue it doesn't really matter. "Musings" suggests that he can see Mulder as some sort of surrogate son, even if he isn't his real son.

There is a strong argument for saying that all the other reasons are just false justifications and rationalisings put out by CSM to cover the fact that he just doesn't want to kill the son of his old friend.

Of course, he tried to kill him in "Anasazi" (Or did he? The soldiers told him Mulder wasn't in there) but every relationship has its bad days.

Whatever. However, as of "The End," CSM seems to have transferred his fatherly sentiments to Spender, and is talking all gleefully about what fun it is to break Mulder's spirit, so I suppose this explanation is no longer valid.


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