A Ship like the one Scully had seen in Africa is found in Canada by a cult that believes aliens are God. William proves to be the chosen child of an alien prophecy: he is to be the aliens' leader, but for this, Mulder must die. The Supersoldiers have been in existence since decades and have infiltrated the FBI. It is implied that Scully became able to conceive thanks to her contact with the African Ship.
These two episodes offer many keys to understanding the whole of the seasons 8 & 9 mythology. This should be a good thing, but the revelations that are made are really uncharacteristic of what XF had gotten us used to: this show didn't use to be about the main characters being the focus of ancestal prophecies of cosmic proportions. Carter and Spotnitz may have tried to save this, but these two are undoubtedly the worse mythology episodes of the series. By the time these episodes were in production, the decision had been taken to cancel the show at the end of the season. So without further ado, let's get on with it.
The Prophecy and William's conception
The Prophecy of the alien Colonists is fully revealed here. It goes like this:
1) William is destined to be the leader of the aliens when colonization comes (Josepho: "your son will lead this alien race."). This will happen if Mulder is dead (Josepho: "if [Mulder]'s alive he's the one thing preventing your son's true destiny")
2) If Mulder is alive then William may follow a different destiny and prevent the colonization (Comer: "Josepho believes your son will follow in his father's paths and try and stop the aliens' return").
With this knowledge, lots of things can then be explained:
- 8X15: DeadAlive: Krycek wanted William dead because, with Mulder's life in the balance, William represented a threat to the resistance against colonization
- 8X20: Essence: Krycek, still fighting for the resistance, wanted to protect the birth of William because, with Mulder alive, William could become an ally in the resistance
- 8X21: Existence: Krycek, now having abandoned all hopes for resistance and following orders from Knowle Rohrer (ie the Supersoldiers, ie the Colonists), wanted Mulder dead to fulfill the prophecy with William the leader of the Colonists
- 9X02: Nothing Important Happened Today II: Mulder went into hiding because the Supersoldiers were after him, to get rid of him and to have William become their leader
- 9X08: Trust No 1: Same with the Shadow Man, who was trying to reach and kill Mulder
- Provenance: Mulder is presumed dead and William was to become the leader of the Colonists; Comer, believing Josepho's findings and pretending to agree with him but in fact acting against the Colonists and in favour of the salvation of mankind, wanted William dead
- Providence: Josepho, a follower of the Colonists, wanted Mulder dead and William safe
The origins of Supersoldiers: plan A
The teaser of Providence reveals that Supersoldiers were in existence back in 1991. Josepho was a Marine in the Gulf War (Operation Desert Storm). On February 26, 1991, he witnessed an event that he wasn't supposed to see: four Supersoldiers working as Marines carrying out an impossible mission.
Here we meet another Supersoldier, betrayed by the lump on his neck (that only the viewers see): the Toothpick Man -- an even more improbable name than the Well-Manicured Man! He is much older than the other Supersoldiers we know (Rohrer, McMahon) and seems to be working high inside the FBI. Perhaps he is working in the same position that the Cigarette-Smoking Man was, in the Treasury Department (7X11: Closure), taking his place after he 'retired' (7X22: Requiem or earlier). This is consistent with the Supersoldiers taking over the power vacuum left after the Syndicate was burnt down (6X12: One Son). It also points to the fact that the Supersoldiers project is even older. Surely the man that became the Toothpick Man could not have been abducted while in a prominent position and returned a Supersoldier a few months later without raising any questions; for the same reasons why Rohrer was turned into a Supersoldier right after his Marine service, the Toothpick Man became a Supersoldier at the beginning of his career. Given his age this could have been as early as the 1950s, perhaps in 1947 right after Roswell. The Supersoldiers, then, have been infiltrating human society for decades. They were the Colonists' initial plan for the preparation of colonization; the Syndicate occurred in 1973 and was something that was imposed on them, as a plan B. But Plan A was kept for safety reasons: the Supersoldiers were sleeper agents, who became really active only after the Syndicate disappeared.
Following his Iraqi encounter, Josepho believed he had seen in the Supersoldiers emissaries of God. He uses words from the Bible to describe his encounter: "Behold, a whirlwind came out of the north and a brightness was about it. And out of the midst came the likeness of four living creatures and they had the likeness of a man." Scully says it's from Ephesians when it's actually from Ezekiel (1:4-5). "The Bible, describing giants who walk the Earth. Who'd believe it? Only the faithful, and we who have seen them, these Supersoldiers, the true Sons of God." We can extrapolate this to understand the hierarchy of the Colonists.
The Ship and Josepho's cult
Josepho created a cult (very much like Absalom from 8X14: This Is Not Happening; even music from that episode is used here!), described as "a religious group, some kind of whacked-out UFO cult", a cult that worshipped the alien Colonists and the Supersoldiers as divine. Josepho has come to "believe an alien race will rule the world" and for him the destiny of mankind, as subservient to the aliens, is obsolete. He does not care whether saving William and killing Mulder means mankind's destruction if this can bring him closer to God. For the "last six months", FBI Agent Comer was sent undercover to investigate the cult's dubious intentions. Comer came to believe what Josepho was saying, but he didn't join him in his worshipping of the aliens, preferring to act against them to save mankind.
Josepho eventually found in Alberta, Canada, an alien Ship like the one Scully found in Ivory Coast (6X22: Biogenesis). "One day God told Josepho to lead us a thousand miles north to find a ship buried in the ground." The Colonists aren't known to impersonate God to speak to people, so instead what might have happened was that in his searches for God and the aliens, Josepho came into possession of one of the resurfaced artifacts of the Ship, just as Dr. Merkmallen in Biogenesis. Unlike Dr. Sandoz who had Albert Hosteen to translate the inscriptions, Josepho did not speak Navajo. As seen in 7X03: The Sixth Extinction, such Ships are very powerful and can give visions to people they choose to. From this initial artifact, Josepho was given visions he interpreted as the word of God; this led to him to the buried Ship and to his knowledge of the prophecy. "Josepho believes that that Ship is a temple which houses the physical manifestation of God."
Through the eyes of Reyes we see the awe of all the discoveries made in the Biogenesis trilogy all over again, nothing new here. "Text from the Bible, from the Koran, scripture from religions around the world." "Writing. Words. Powerful words." "And science, too. The periodic table of elements." "Millions of years old", "based on radiometric readings from fossils that were encrusted on the surface of the Ship."
How William came to be
Though not straight-out stated in the dialogue, like so many things in the X-Files, these episodes make one more revelation (or confirmation): how Scully became pregnant. Essence/Existence established that William's conception was from a natural union between Mulder and Scully: no manipulation from the Cigarette-Smoking Man in 7X15: En Ami, no fertilization from Zeus Genetics in 8X08: Per Manum. Moreover, Nothing Important Happened Today and Trust No 1 show a Scully who believes that her child is normal, confident that it was born naturally. What remained to be explained was how Scully, who was declared barren (5X05: Christmas Carol), was able to conceive. This question still torments Scully, while her mother tells her not to question God's miracles: Margaret Scully: "God has given you a miracle. A child that wasn't supposed to be. Maybe it’s not to question, just to be taken as a matter of faith." Scully: "Mom, I can't take this on faith. I need to know. I need to know if it's really God I have to thank." The tone is set: if God is not to thank (and despite signs of life after death we have never seen any actions that have to be explained by divine intervention in the XF mythology), then who is?
From all this it transpires that Scully was given her fertility back when she came into contact with the Ship in Biogenesis. It is only fitting that what allowed the creation of the alien prophet should have been set up by alien forces. If we continue extrapolating, if William the miracle child is Jesus and Scully is the virgin Mary (see the heavy religious imagery in Existence), then the Ship, the mechanical envoyé of the divine Purity, is God's messenger the Angel that impregnated Mary with Jesus. William is explained biologically as the child of Scully and Mulder, but indirectly and symbolically it's the Ship/God that gave Scully this child.
More machinations at the FBI and religion
Josepho learnt of the prophecy, identified who William and his parents were, and started plotting Mulder's death so that the prophecy would be realized. He sent "threats on Agent Mulder's life" to the FBI. Eventually there were unconfirmed reports that "Mulder was already dead"; suspicions were that "they killed him to fulfill this prophecy." The FBI chose to hide this from Agent Scully in order not to cause her too much pain (isn't that cute of them?). Josepho has William abducted and brought to the Ship. But even Josepho isn't sure that Mulder, who's been living really well hidden it seems, is dead ("I believed he was dead, but now I have reason to doubt that. And if he's alive he's the one thing preventing your son's true destiny."). Then comes the worse line of the entire series: "If you want to see the boy, you'll bring me the head of Fox Mulder." Throughout season 9, Scully's new hair make-up and her leather outfit might have made her sexier, but crying in each scene is somewhat irritating.
Much religion in this episode, and not only from the aliens-God correlation. Reyes uncharacteristically goes to a chapel to prey for the hospitalized Doggett. And Doggett, while in a coma, has an experience that shakes his sceptic view on life. "I heard someone talking." "This voice in my head, it was... it was talking to me telling me to get up, telling me to warn Scully about this man [Josepho]" "They're going to come to you [Scully], but you can't trust them." We can only make guesses as to who this spirit was. It is possible this was the action of a Walk-in spirit (7X11: Closure), warning of potential suffering of an innocent soul, in this case William; how William would suffer though is unclear. It's more possible that some other soul, not a Walk-in, was warning Doggett (like the dead that Mulder sees in 9X19/20: The Truth): more specifically, Agent Comer. The Toothpick Man had just killed Comer in the immediately preceding scene and stolen the artifact that was protecting him. The final scene, the Toothpick Man in Kersh's office, makes it clear that though Kersh is tough with Assistant Directors Skinner and Follmer under him, Kersh answers to the Toothpick Man. The Supersoldiers are fully in charge of the situation.
Margaret Scully: "I know you're worried about him. That there are things about him that you just can't explain. But even if you were to get those answers, what would it change?"
Scully: "Mom, he's my child."
Margaret Scully: "And you have to love him and raise him in spite of everything. Dana, God has given you a miracle. A child that wasn't supposed to be. Maybe it’s not to question... just to be taken as a matter of faith."
Scully: "Mom, I can't take this on faith. I need to know... I need to know if it's really God I have to thank."
Josepho's teaser voice-over: "The Bible says God appeared to Moses in a burning bush. He came to Jesus on a mountaintop. For Buddha, God came while he sat under a tree. God came to me in a vision in the desert, February 26, 1991. [Operation Desert Storm] My recon squad had engaged Saddam's army in a small Bedouin encampment. We'd been ambushed, taken all by surprise, and there were casualties. We were holding our perimeter, and we might've held up; but on this day, I had a terrible sense of foreboding and I saw the future of those brave men, and they were about to die. Death came to take my men. But not me. I was left as a witness to a vision. [Supersoldiers appear] Angels from Heaven. 'Behold, a whirlwind came out of the north and a brightness was about it. And out of the midst came the likeness of four living creatures, and they had the likeness of a man.' I knew why my life had been spared. That I was to deliver the message of these angels -- these Sons of God -- to deliver the message of the God who came before all other gods."
Reyes: "Your child was a miracle, Dana. I don't doubt that the things I've witnessed are any less miraculous. But your son is not an abomination, a thing that should cease to exist. You tell me on that Ship is written scripture from the world's great religions. Tell me a religion that decrees the death of a child. Not just your child but any child. This is a man saying these things to us. How many religions warn of false prophets? Men sent to deceive us?"
Josepho: "If you want to see the boy, you'll bring me the head of Fox Mulder."