Scully's term approaches its end. The alien facsimiles, the Supersoldiers, destroy Zeus Genetics, who after all had nothing to do with Scully's pregnancy but considered the baby a miracle. Krycek explains the baby is a threat to the aliens' colonization plans. Mulder suggests the baby is a gift from God. Knowle Rohrer implies that the baby is an organic version of the Supersoldier. Feeling threatened by the Supersoldiers, Scully is taken to a secret location; with the help of Reyes she delivers safely, under the eys of many silent Supersoldiers who apparently meant no harm. Krycek abandons all hope and collaborates with the Supersoldiers; he is killed by Skinner. Scully and Mulder rejoice with their newborn son, William.
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).
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.
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.
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".
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' 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".
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.
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.
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).
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.
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."
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.
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.
Mulder's teaser voice-over: "We call it the miracle of life. Conception: a union of perfect opposites, essence transforming into existence, an act without which mankind would not exist and humanity cease to exist. Or is this just nostalgia now? An act of biology commandeered by modern science and technology? Godlike, we extract, implant, inseminate, and we clone. But has our ingenuity rendered the miracle into a simple trick? In the artifice of replicating life can we become the creator? Then what of the soul? Can it, too, be replicated? Does it live in this matter we call DNA? Or is its placement the opposite of artifice, capable only by God. How did this child come to be? What set its heart beating? Is it the product of a union? Or the work of a divine hand? An answered prayer? A true miracle? Or is it a wonder of technology, the intervention of other hands? What do I tell this child about to be born? What do I tell Scully? And what do I tell myself?"
Doggett: "What is it exactly we're looking for being I'm starting to piss a lot of people off, Mr. Mulder?"
Mulder: "Pissing people off comes with the territory, Agent Doggett. It's part of working on the X-Files."
Scully: "Look, Mulder, look, I can't take this! I can't live like this, as, as the object of some unending X-File."
Mulder: "This isn't about the X-Files, Scully. It is only about you."
Doggett: "You realize you're all listening to someone who tried to kill me. He left you for dead."
Scully: "I don't believe this."
[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?"
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?"