Since the season 8 was largely planned as a whole from the beginning, many things seen over the season don’t make sense without the keys given in this two-parter finale. And of course there are some left-over mysteries to give the season 9 mythology something to do. This could have been the great finale of the X-Files, and while there are some good bits there are others that feel forced — and I’m not only referring to the shippy bits. Not one but two car chases in the FBI garage (which don’t really make sense and are completely inconsequential: if the Supersoldiers can’t be killed and they set out to kill Doggett or Skinner, then there’s no reason why they should escape in the long term). Like in 8X01: Without / 8X02: Without and the desert scenes, here there are endless scenes in the same setting, the FBI building: characters coming, going, talking, walking away, popping up again… absurdly obvious religious overtones… (it started well with Essence though).

Is the recurring joke about pissing people off meant to be taken personally? Both episodes were written by Carter; despite all good intentions, this stands up to a series finale even less than 7X22: Requiem.

The Supersoldiers: alien or military?

From 8X15: DeadAlive and 8X18: Three Words, we know that many humans were abducted and replaced by similar-looking “alien replicants“, basically human bodies with an alien conscience. Billy Miles is not the only one: intelligence agent Knowle Rohrer is one, here we learn that FBI agent Crane (seen in Within/Without) is one, as is the Game Warden that Scully and Reyes come across, and all these silent witnesses to Scully’s delivery. Rohrer and Crane’s night meeting with Kersh, along with Krycek’s comment that it goes “right into the FBI” raises suspicions that Kersh himself might be one of them — but as we’ll learn later he’s ‘just’ following orders and that these aliens are infiltrated in higher places in the hierarchy than him. They are “virtually unstoppable” (they survive bullets and being mashed up into hamburger meat through a garbage truck), more resistant than humans or Alien Bounty Hunters. They have a metal vertebra that seems to be the only essential part of them: out of this vertebra they can reconstruct their entire body through ‘magic’ replication (defying all known laws of physics at the same time!). Perhaps that is where the alien conscience resides, the essential ‘centre of operation’. Krycek: “They want to knock out any and all attempts by us to survive the final days, when they come back to retake the planet“, “created to aid in the repopulation of the planet“. They are here to replace the Syndicate and the army of hybrids: to prepare the way for colonization and make sure it happens successfully (3X24: Talitha Cumi, One Son). That means eliminating any kind of resistance to colonization. Everything seems clear.

Billy Miles’s actions confirm that the Supersoldiers have a conscience that is not human but alien. Faithful to the Colonists’ obsession with genetic purity, Supersoldier Billy calls the alien baby Dr. Lev holds an “abomination“. But are not the Supersoldiers themselves a result of an abominable gene slicing and dicing, a mix of Black Oil DNA and human DNA? This can only mean one thing: the Supersoldiers might be a new artificially created race with a conscience that is proper to them (ie not human), but the Colonists (ie Purity, the Black Oil, the greys) do not consider them as equals. As their name suggests, the Supersoldiers are merely following orders from above, genetically impure beings that prepare the way for their masters. The ‘green-blooded’ alien/human hybrids were treated as an inferior race separate from humans as well (2X16: Colony, 3X24: Talitha Cumi). The Supersoldiers are the new slave race of the Colonists.

But at least they seem fine with it: perhaps they are allowed less free will. Elements of the human mentality remain (Knowle Rohrer) but the alien orders take precedence.

Knowle Rohrer spreads much misinformation in his talks to Doggett. By telling him stories of Supersoldiers developed by the military, he fuels his scepticism to all things alien. Rohrer tells him this all comes from “a rumored program out of the Cold War, a plan to create a Supersoldier” of which Billy Miles would be “a prototype“. As Deep Throat used to say, a lie is best hidden between two truths; there was indeed a program to create a new kind of soldier, a ‘super-soldier’, through medical enhancements (2X04: Sleepless), genetic manipulations (1X10: Eve) or even through experiments with alien DNA (3X10: 731), and probably more, but he and Billy Miles are certainly not part of it. Everthing he says about Scully has elements of truth, nicely reformulated to pass down a false story. “She was part of a program herself. Six years ago, Agent Scully was taken in a military operation staged as an abduction. They put a chip in the back of her neck to monitor her.” So far that’s true (2X06: Ascension). “[The chip] was also used to make her pregnant with the first organic version of that same Supersoldier.” That’s another theory to explain Scully’s pregnancy that will prove to be a fabrication: Rohrer is referring to every woman abductee but Scully, as will be explained in 9X01/02: Nothing Important Happened Today — however the term ‘Supersoldier’ will be used to describe them afterwards, despite their alien origin.

Life and times of Zeus Genetics

Lizzie Gill, “research scientist” at Zeus Genetics, spills the beans on their work: they were “trying to produce human clones, long before the media circus with sheep and cows” (referring to the first successful cloned mammals, Dolly the sheep in 1997 and Daisy the cow in 1999). Drs. Parenti and Lev were officially working as OB-GYNs trying to “prevent children with non-survivable birth defects“; the embryos or babies in jars in the ‘showroom of horrors’ are just that, deformed human babies.

But on top of that, with money and orders “from government men“, they researched human cloning, based in “an illegal medical facility” inside a warehouse. Lizzie’s revealing “they’re all dead now” points to the fact that these men were Syndicate elders, all dead since 6X12: One Son. Duffy Haskell, working in a black program inside the governent, was Zeus’s tie with the Syndicate. The Syndicate provided Zeus with alien genetic material (“DNA that the government had since 1947“, since Roswell), which Zeus used to create new cells and babies: “We were surprisingly successful with a clone from a human egg and alien DNA“. Their success was cloned “alien babies“. To be precise, these aren’t 100% alien babies though. If one was to clone an alien, there wouldn’t be human material involved. The fact that they used human eggs makes these babies, even slightly, human (in that sense they are ‘slightly’ hybrids). In a procedure similar to that used to create the familiar ‘green-blooded’ hybrids (see 2X16: Colony), they took off the nucleus (containing the human DNA) from a human egg and inserted the alien genome. The rest of the egg — including for example the mitochondrial DNA, which is separate from the nucleus and is passed on from mother to child — is human. Also, the embryo didn’t grow in an alien environment but inside a human woman, exchanging bodily fluids with her, finally “birthed by human mothers desperate to conceive“.

Even if these babies are not fully alien, they are alien enough. “They didn’t live more than a couple of days, but tissue and stem cells is what we were after for other experiments.” The end goal of these experiments was to obtain tissue, stem cells and alien genetic material for further experiments. Which were those? “I don’t know anything about that. But I know it was something good.” Lizzy’s naiveté aside, this material was used in other experiments conducted by the Syndicate, for the purposes of creating an alien/human hybrid (3X10: 731, One Son, among others). After the Syndicate was destroyed, “the work continued“, Zeus Genetics working freelance without any supervision, the scientists fueled by their passion for their interesting work.

Organic Supersoldiers and Scully’s baby according to Zeus Genetics

But after the Syndicate, the alien replicants took over that vacant seat of power, and started redirecting the efforts that were dedicated to hybridization towards their own ends. Zeus Genetics was manipulated into working towards the creation of one of those alien replicants, not in the form that we see them, like Billy Miles, but in a different, organic, form. What Rohrer says about Scully’s baby can be taken to refer to this program’s goal: “the first organic version of that same supersoldier“.

Indeed Lizzy says that what they were trying to create in a lab was “a perfect human child but with no human frailties” — something that fits the description of what a Supersoldier (as in a powerful and invincible soldier in an army) should be. The alien replicants like Billy or Rohrer were created from the alien Colonists themselves, using their own genetic material. What Zeus Genetics set out to do was to create a perfect being that, in the end, would be like these alien replicants. The precision “organic” means that there is something different with them. The “organic version” would characterize the means to achieve it: through some kind of progressive, smooth, gene therapy — as opposed to the violent tests and skin shedding of the ‘non-organic’ replicants. Since there is gene splicing between human and alien material, one could say this is about making an alien/human hybrid as well, but these Supersoldiers and this organic Supersoldier would be a very special kind of hybrid — human in appearance but not conscience and strength.

It then becomes clear that Zeus Genetics believed that Scully’s baby was just that: “a perfect human child but with no human frailties“. The doubt from 8X08: Per Manum dissipates: this child was not conceived artificially in a test tube and implanted in Scully’s womb (“One could only hope to create that in a lab“). This child was conceived completely naturally, and that is what attracted the interest of Zeus Genetics: “There’s nothing wrong with her! […] The child she is carrying is very special“. Zeus Genetics came across the end result of their research in a baby that occured outside a lab! After the events in Per Manum, Scully left Dr. Parenti and found another doctor to follow her pregnancy (“with my new doctor that I trust implicitly“).

Zeus Genetics didn’t abandon her though, they worked actively to remotely monitor her pregnancy (“A Dr. Lev and a Dr. Parenti working with this Duffy Haskell monitoring Scully’s pregnancy“). Lizzy, recruited by Scully’s mother, passes as a maid, a position from which she can follow out the rest of the pregnancy. They are doing everything they can “to protect her” and to have the best result as possible. Lizzy switches Scully’s medicine, but this proves to be a false alarm: she just substituted them with harmless “vitamin supplements […] nothing you’d be afraid to give any expectant mother“. For them, Scully’s baby is nothing short of a miracle.

Zeus Genetics’ work is cut short by Billy Miles, who, Terminator-like, executes its members one by one (Lev, Parenti, Haskell) and burns their installations to the ground (the clinic seen in 8X08: Per Manum). Only Lizzy escapes. Why he did that, when Zeus Genetics had just been following orders from the Supersoldiers? It’s possible that with Scully’s baby coming to term, the Supersoldiers no longer needed them. Another explanation is given in 9X01/9X02: the chloramine project was completed.

Scully’s baby according to Krycek

And then Krycek comes out of nowhere to save the day. Krycek, somehow, has answers about Scully’s baby. Perhaps by reading the artifacts and the scanned photos (from Kritschgau’s computer) from the Ship from 7X04: Amor Fati. Krycek agrees with Zeus Genetics: “Your baby was a miracle. Born of a barren mother’s barren womb.” In DeadAlive, Krycek wanted to kill Scully’s baby for some unknown reason; he explains himself as “I wanted to destroy the truth before they learn the truth“.

“They didn’t even know about it. I don’t know exactly how they could have found out just how, how important it is, how special.” Through Zeus Genetics, the Supersoldiers/Colonists have learned of Scully’s child. Krycek believes that the aliens are afraid of the baby because “they’re afraid of its implications, that it could somehow be greater than them. Something more human than human“. Ultimately, this higher force is an actor that the Colonists would be uncomfortable with, so they consider Scully and her child a threat. This explanation would imply that the aliens had nothing to do with the conception of Scully’s child, and that they are afraid; this is a highly unsatisfying explanation that will be cleared out with 9X10: Provenance / 9X11: Providence.

Krycek: “to aid in the repopulation of the planet.” Mulder: “Which Scully is a threat to.” Krycek: “If she has that baby.” But if it’s a threat why do the Supersoldiers ultimately allow the child to be? All of this doesn’t make sense without the entirety of the prophecy as revealed in 9X11: Providence. Every character acts only thanks to the information he/she has got, and even Krycek doesn’t know the whole truth. Scully’s baby is special and powerful, a much-desired ally that lends power. Krycek believes that it will join the side of whoever gets to him first: Colonists or Resistance. In DeadAlive, the Colonists didn’t yet know about the baby. Krycek wanted to get rid of that potential menace before it would see the light of day. The vaccine for Mulder is just a ploy to get to an end: Krycek’s prime goal was not saving Mulder but killing Scully’s baby. He failed. The Colonists learnt of Scully’s baby, and now at all costs they must be prevented from reaching it, if Resistance is to have a chance.

Krycek’s demise

Since the beginning, Krycek is consistently fighting for the Resistance (well, for his own salvation, but let’s just say that these goals coincide most of the time). In Essence he’s still acting with that on his mind. In Existence, however, something happens that makes him change his mind. Krycek has a meeting with Knowle Rohrer in the FBI garage. What Rohrer tells him makes Krycek abandon all hope. Rohrer quite possibly told him that he is a Supersoldier, and that Supersoldiers are infiltrated in all the influential spheres of the government, the federal agencies like the FBI, the local law enforcement (eg the Game Warden). The Supersoldiers hold much more power than what Krycek previously though; they have the power already, and there’s nothing Krycek can do to prevent that now. Resistance is futile. Perhaps Rohrer threatened to kill him right there right now. Krycek cornered, he had no choice but to cooperate.

Rohrer told him all of that because Krycek was the leader of the Resistance, and because he can reach Mulder. It’s possible that Rohrer told him the whole of the prophecy (9X11: Providence), of which Krycek knew only a part. Without Mulder, the baby will become the leader of the colonization, an ally and an important figure for the Colonists.

Only if Mulder lives to protect the baby will the baby become a great threat to the colonization schemes. Mulder must die. Rohrer asks Krycek to kill Mulder. In exchange he probably offered him survival after the colonization (an agreement similar to the one the Syndicate made back in 1973). Krycek wants to save himself, and to hell with the rest of the world. Krycek finally turns to the same side as the Cigarette-Smoking Man: if resistance is impossible, then survival is the ultimate ideology.

Krycek’s last conversation with Mulder is full of bitterness. He’s the Ratboy, but when it comes to the Resistance, he and Mulder were brothers in arms: “I’m the one that kept you alive, praying you’d win somehow.” Krycek is Mulder’s alter-ego, a brother that chose a different path: “We wanted the same thing, brother.” Krycek would like Mulder to join him in the ‘dark side’, let go of the ideal of the impossible Resistance (“The tragedy’s that you, you wouldn’t let it go“). But Mulder won’t. Then Skinner comes, shoots Krycek. Krycek tries to convince Skinner to kill Mulder. You can’t fight the future: “It’s going to take more bullets than you can ever fire to win this game“. Krycek offers Skinner what the Supersoldiers offered Krycek: “[kill Mulder] and I can give you a thousand lives!” This essentially means that Krycek would be given something close to immortality; immunity; healing powers; maybe he would be turned into a Supersoldier. Survival is only possible by collaboration and replication. Skinner doesn’t buy into it and gets some revenge for all the suffering he’s taken from Krycek (3X01: The Blessing Way, and particularly the nanotechnology deal in 6X10: S.R. 819 and 7X04: Amor Fati). Skinner kills Krycek (along with an exceptionally non-XF-like cheesy shot following the bullet).

The Ratboy is no more (which, for me, is an aberration; the CSM can die, but Krycek should find ways to survive). At least it’s suiting enough that Krycek leaves the series at the same time Mulder is.

There is one sentence that bears particular significance: “I’m the one that kept you alive“. Considering that Mulder was dying (8X01: Within) and he ended up being cured ‘thanks’ to his abduction (8X18: Three Words), could it be that Krycek allowed Mulder to be abducted in 7X22: Requiem? By doing this, he makes sure that Mulder is alive and kicking and still part of the Resistance, an ally. Of course Mulder’s conversion into a Supersoldier would have to be prevented, and that’s what Krycek initially intended with the vaccine in DeadAlive. But other priorities took over: Scully’s baby. It’s a theory that relies on a big series of events that could have gone wrong (Mulder dying, Mulder not being taken out of its grave in time…) but it would explain Krycek’s lack of action in Requiem — even though that would be stretching a lot what a Krycek freshly out of jail in Requiem would know and anticipate that far.

William

The Supersoldiers’ actions can only be understood if they believe that Scully’s baby can become their ally. Throughout, they try to reach Scully, not to harm her but just to assist her. Agent Crane draws the attention of Doggett into chasing after Billy Miles in Parenti’s office, when in fact Billy chases Scully in her home. Billy then chases her in the FBI building. When he fails, Agent Crane allows them to escape because he knows how to reach them later on. Everybody believes that only Doggett and Reyes know where Scully is going to deliver, but Doggett and Reyes’ phonecall was monitored: “There’s no way Crane can tap calls in here, Mulder. He’d have to have access to the communications system.”

But indeed he did. And judging from the advanced surveillance the Supersoldiers have access to (9X08: Trust No 1), it’s not surprising at all that a Supersoldier, the Game Warden, finds Scully and Reyes — and tries to gain their trust by faking the killing of Billy Miles. In the crucial moment, Scully delivering her baby, many Supersoldiers arrive. Instead of harming anybody, as the viewer was set up to believe, they just watch and leave: “they came to take him from us; why they didn’t?” Mulder offers a calming explanation: “maybe he isn’t what they thought he was“. That would have been a letdown that wouldn’t explain anything! The baby was really special, and all the Supersoldiers did was to make sure that it came into the world safely. The Supersoldiers wanted no harm to be done (Game Warden: “This baby will be born“).

Were the aliens afraid? Was there something superior at work? Existence has many religious overtones, and not very subtle at that! There is a light above the place where the baby is born, like the star above Jesus’ crib (could the light be an alien ship overseeing the scene?). Mulder follows the light like the three Magi followed the star (“There was a light. I followed it.“). Scully gives birth when she was believed to be barren, paralelling Virgin Mary. The Game Warden says she’ll fetch “swaddling“, a rather archaic term for a child to be born in 21st century USA. There are even the three gift-bearing Lone Gunmen, like the three Magi. Given how the aliens have been represented for God before in the series, the line between the actions of the aliens and evidence of a divine power is a fine one. With Krycek’s ‘explanations’, Mulder offers that the very reality of this child occuring in nature would be proof “that there’s a God, a higher power” that they fear. This is the first time we hear that the Colonists fear anything and; this explanation offers one more theory about Scully’s pregnancy: that there really is a God, and William is his gift.

However, the references to christian religion may be there for ‘subtly’ representing the importance of this birth, but as far as the mythology of the show is concerned (and as we’ll come to understand later), the aliens were just witnessing the birth of their leader. For the Supersoldiers, the birth of their future leader was a very important, religious moment, they wanted to assist to as a kind of pilgrimage. An addendum to that may be that the Supersoldiers did indeed fear a superior power, that of what has come to represent God in the show, that which is the master of the Supersoldiers: Purity or Black Oil, or the Colonists themselves. As the leader of the (alien) Supersoldiers, William may be the mediator between the Supersoldiers and the Colonists themselves.

Meanwhile, Reyes has joined the X-Files as per Doggett’s request (Scully saying that Reyes reminds her of her sister Melissa was a nice touch). They launch an investigation into Kersh. Doggett has become the leader of the X-Files, and he shows that very well by displaying a muleheadedness and resolve as strong as his predecessors’.

Out of all the different red herrings and possible explanations that are offered throughout, only one transpires as the true one: Scully’s baby is the first organic Supersoldier, conceived naturally, and holding a special significance for the Colonists. This pregnancy may have been another reason why Scully was not taken in 7X22: Requiem. The ‘organic Supersoldier’ baby thread will be further explored in 9X01/02: Nothing Important Happened Today II and 9X08: Trust No 1. Funny that not even Mulder was sure of who the father is as late as Essence! Carter wanted to tease the audience to the very last moment. But it only makes sense that the child is Mulder’s! “The truth we both know.” His name shall be William, “after your father” (and incidentally Scully’s father as well). Mulder and Scully are allowed to share their love (even onscreen!) in the few closing moments of the season. A desperately happy and soppy ending that might have rejoiced the shippers but in fact gives more questions than answers. After all this, films or a ninth season were necessary to provide (unsatisfying?) answers… A scene that epitomizes the X-Files better is a short conversation between Mulder and Doggett, reflecting the motel scenes in 7X22: Requiem and 9X19-20: The Truth: Doggett: “Where the hell is it all going to end?” Mulder: “I don’t know. Maybe it doesn’t.” Scully and Mulder have sacrificed a lot yet keep on fighting unabashed.

Essence

Existence

[around Billy Miles’ hamburger body remains]
Assistant: “Your order was to establish and confirm real fact of death.”
Pathologist: “I’d say he’s dead. How about you?”

Doggett: “And then what? How long can you keep this up? How long until the next Billy Miles rears his head? The next threat? The next phantom? You ever stop to ask yourself? All the sacrifice, the blood spilled. You’ve given nearly a decade of your life. Where the hell is it all going to end?”
(Mulder thinks)
Mulder: “I don’t know. Maybe it doesn’t.”

Krycek: “Doesn’t seem fair now. Doesn’t seem right. Coming down to this.”
Mulder: “What do you know about fair or right, Krycek? You’re a coward.”
Krycek: “I could’ve killed you so many times, Mulder. You’ve got to know that. I’m the one that kept you alive… praying you’d win somehow.”
Mulder: “Then there really is no God.”
Krycek: “You think I’m bad. That I’m a killer. We wanted the same thing, brother. That’s what you don’t understand.”
Mulder: “I wanted to stop them. All you wanted was to save your own ass.”
Krycek: “No. I tried to stop them. Tried to kill Scully’s baby to stop them. It’s too late. The tragedy’s that you, you wouldn’t let it go. That’s why I have to do this. ‘Cause you know how deep it goes. Right into the FBI.”
Mulder: “You want to kill me, Alex, kill me. Like you killed my father. Just don’t insult me trying to make me understand.”
(Hesitation. Skinner shoots Krycek. Twice.)
Krycek: “It’s going to take more bullets than you can ever fire to win this game. But one bullet… and I can give you a thousand lives! Shoot Mulder.”
(Skinner shoots Krycek dead.)

Scully: “This is my baby!”

Doggett: “I assume it because this office is under investigation.”
[…]
Kersh: “You investigate what I tell you.”
Doggett: “And you put me on the X-Files. That’s what I’m investigating.”

Mulder: “I think what we feared were the possibilities. The truth we both know.”
Scully: “Which is what?”
(They kiss.)