THE COLONISTS' MOTIVES IN SEASON 8

In Within and Without, the Alien Bounty Hunter was dispatched to retrieve not only the former abductees (or those who suffer from encephalitic trauma courtesy of alien technology, i.e. Mulder), but also Gibson Praise: a successful, natural alien-human hybrid. Although not technically a hybrid, his latent alien DNA had been (somehow) unlocked, enabling him to utilize telepathy.

Gibson, then, had become a Cassandra Spender-level threat. He barely escaped, forced into even deeper hiding to save his life.

In Per Manum, the aliens-- ala the super soldiers-- systematically annihilated alien-human hybrids created by former-Consortium (or remnant Syndicate) research. They used Scully to track down Mary Hendershot, intercept her delivery, and swap a "real" human baby for the hybrid Mary was carrying.

Alien-human hybrids, or babies created through alien technology, were the second threat the aliens targeted in Season 8: reclaimed by any means necessary and (as we later learn in Essence) destroyed.

In This Is Not Happening, the aliens hunted down Jeremiah Smith, one of their own who had defected to help the human race. They successfully thwarted his aims and recaptured him-- and likely exterminated him (he never appeared in canon again.)

Jeremiah Smith, like Josh Exley, was the third threat eradicated: a friend to the enemy, he had become a liability.

In Deadalive, Krycek warned Skinner that the groups he represented demanded either Mulder-- who had been stalled from turning into a super soldier-- or Scully's baby-- who, the aliens suspected, was created via their technology (i.e. the downed craft in Africa)-- killed. It was a false choice, one Krycek cooked up when caught red-handed. In reality, the forces-that-be likely wanted Mulder dead (William would be dealt with later.)

Humans studying one of their Frankenstein-ed abductees and potentially figuring out how to reverse his "virus" was a fourth threat; and it was safer, the aliens would have deemed, to eliminate Mulder immediately.

Three Words set a clearer precedent: Absalom, who had worked alongside Jeremiah Smith to save returned abductees, was left in the hands of the FBI (and, it's hinted, the Syndicate peons.) Super soldier Knowle Rohrer materialized to manipulate Doggett into sending Mulder to his death; but even then, Mulder was the target only incidentally.

Absalom merely roused disinterest in the aliens: he was beneath their consideration because of his 'lack' of alien DNA or access to advanced technology. Their reaction to William's arrival in Existence is strikingly similar: immediate, concordant apathy.

In Essence, the aliens sent Billy Miles to burn down the Consortium clinics producing alien-human hybrids (and to murder their doctors, Parenti included.) Duffy Haskell (from Per Manum) was also slaughtered-- and Lizzie Gill targeted-- for working alongside the Syndicate to monitor Scully's pregnancy.

The clinics were the fifth threat to the would-be colonists.

In Essence, the aliens dispatched Krycek to thwart Mulder and Scully's escape, sow doubt, and expertly separate both agents. The super soldiers continued working hand-in-glove with Krycek until his untimely death, then redoubled their efforts to keep Mulder and Scully further apart (i.e. car chases at the FBI) until William was born.

Why? Because, as Season 8 laid out multiple times, the aliens believed any human-- full-blooded (Gibson) or not (hybridized babies)-- with activated alien DNA would pose a threat to their colonization timeline. That was the ultimate challenge: the root they were trying to tear up.

The plan, then, in Existence becomes plain: isolate Scully; monitor her delivery; and steal her child if it were deemed to be alien or alien-adjacent.

DOESN'T MAKE HIM ANY LESS OF A MIRACLE

Yet when William was born, the super soldiers seemingly lost all interest, trailing dust and silence behind them in steady retreat.

If aliens-- as Biogenesis-The Sixth Extinction claim-- began life on Earth with the future intent to colonize it, then any person born with heightened abilities or through unauthorized technology wouldn't serve their agenda. Truth be told, that person would most likely be perceived as a hindrance.

If the aliens (as Krycek prompted) believed the Mulder-Scully baby was proof of God, then they would have considered him a threat to their control: an unpredictable wrench in their future plans. He would not have been afforded passive surveillance nor unexpected protection (per Season 9's confusing messaging): he would have been snuffed out right before or right after his first breath.

If the aliens believed William posed any sort of threat, or possessed any potential "powers" or abilities that might manifest at any point (ala Gibson Praise), then he never would have made it out of that Georgian cabin.

If the aliens, however, believed William was normal-- that he wasn't imbued with special powers, like Gibson; that he wasn't an alien-human Syndicate hybrid, like Mary's baby; that he wasn't a special Messiah marked by God to save the human race-- then he would have been like Absalom, or Mulder (after he returned to the land of the living): wholly human, and therefore irrelevant.

The beauty of Season 8's ending lies in the last five (or so) minutes. Not only do Mulder and Scully face the future as an unambiguous couple, but they do so while soundly dispelling speculation.

Scully: I don't understand, Mulder. They came to take him from us-- why they didn't....

Mulder: I don't quite understand that either. Except that maybe he isn't what they thought he was. That doesn't make him any less of a miracle though, does it?

And in another rare moment of perfect clarity, The X-Files takes time to erase all doubt:

Scully confesses, "From the moment I became pregnant, I feared the truth... about how... and why. And I know that you feared it, too."

Mulder concludes, "I think what we feared were the possibilities. The truth we both know."

It was, as the writers intended, the end of the Mulder-Scully era; and it was, for once, tied up with an almost too-perfect bow on its head.

A THEORY: WILLIAM, THE DISRUPTED SAVIOR OF THE WORLD

If William was born to be a supernatural figure (or savior) of some kind-- as Frank Spotnitz and Chris Carter imply with stars in the sky and three wise men bearing gifts and the White Buffalo symbolism of his adoption--

"Like the Navajo, these people have their own stories and myths. One of these stories tells of the white buffalo woman who came down from the heavens and taught the Indians how to lead virtuous lives and how to pray to the creator. She told the people she would return one day, then she turned into a white buffalo and ascended into the clouds, never to be seen again. But on this day, when the holy people had given the F.B.I. man a miracle, a white buffalo was born and every Native American knew, whether he believed the story or not, that this was a powerful omen and that great changes were coming." 

--then his disappearance from canon for nearly eighteen years, without any exploration of the global impact of his existence (until Season 11) heavily undermines that message.

William's magical arc could, in a hypothetical world, have worked; but instead, its conclusion was disrupted with the inevitable fracturing of The X-Files's writing team. Frank Spotnitz was co-collaborator with Chris Carter during Season 5 (when ideas for a surprise pregnancy were tossed around), Season 7 (when Scully's healed fertility in The Sixth Extinction and William's conception in all things was plotted), and Season 8 (when Scully's pregnancy and William's birth concluded.) However, the task of crafting Season 9 baton-ed to him in Carter's absence:

July 12, 2001:

Planning for the ninth season began in June with Carter absent for the first time since he created the series in 1993. He has yet to reach a deal with Fox to return for the ninth season and there is speculation he will not return or serve only as a “consultant,” with Spotnitz assuming the lead role for the show’s creative decisions along with co-executive producers Vince Gilligan and John Shiban. ...

“Obviously, we hope he comes back because it’s his show, it’s his vision that we’ve all been serving for all these years and he’s an enormously talented writer and producer,” said Spotnitz, who has been in charge of the series with Carter gone. “If he doesn’t, it’s not like we don’t know where all the files are.”

Despite that, Spotnitz said Scully will be a vital part of the ninth season with one of the central story lines exploring how Scully’s fertility was restored. Another issue to be addressed is how to explain Mulder’s absence given the romantic relationship with Scully that was confirmed in last season’s finale.

To what degree William's "powers" were planned in Existence, we don't know. But we are privy to a civil disagreement between Frank Spotnitz and Chris Carter upon the latter's return-- William's adoption: Carter for, Spotnitz against (initially.)

May 2002:

Leading up to the finale, we had the episode “William,” a very pivotal episode for Scully – and one whose ending begs the question of why have Scully go through the pregnancy arc to begin with.

Spotnitz: Yep. I had a lot of reservations about that storyline and about her giving up the baby, and was not at all sure that it was the right thing to do. But in the end, I think it was the right thing to do, because it becomes unsavory. And I think everybody... felt that this was going to be an obstacle to us in the movies. And I think the solution we came up with was kind of Solomonic in its wisdom in the end, which is, it’s true to Scully’s character and the pattern of behavior that she’s had for the past nine years: that she sacrifices her own happiness for a greater cause. It’s true to the tragic series of losses she’s endured over the course of the series, and I thought it was very moving in the end. It kind of helped us go forward with Mulder and Scully – and whether there are movies or not, it serviced them – and us, as storytellers – in a good way.

Nevertheless, both men went on to co-write I Want to Believe, wherein William's absence played heavily on his parents' conscience: he was palpably remembered as their baby, their son.

That changed when Spotnitz moved away from the series. William was re-introduced in the Revival: elsewhere for Season 10 (until fans pitched a storm), then distant or manipulative (and cruel) in Season 11. Finally, he was haphazardly tossed aside and labeled "an experiment"-- marked as CSM's test tube baby in the finale, then retroactively claimed as both Mulder and CSM's on the unofficial birth certificate (a father-and-son's son?) post-MSIV's uproar.

If William's arc had stuck the landing (per Spotnitz's ideas), he would still possess powers, would not have been adopted out, and would be with Mulder and Scully when colonization dawned-- a fulfillment of some prophecy, perhaps. Or perhaps a child saved from the role of prophecy through his parents' sheer determination (the reemerging fate vs. freewill theme from the original run.)

Of course, there is (as always) plausible deniability: the star in the sky and the three wise men could simply be an ode to Scully's Christianity, while the White Buffalo calf and alien abilities would act as an ode to Mulder's. William's existence (and powers) could simply be a pile of mixed metaphors that don't neatly fit into any prescribed category-- but that could be brushed off, too, with the assertion that life rarely is.

We'll never know the outcome Frank Spotnitz would have edged towards. What we do know is that he, Carter, and the lead actors were hoping for more movies-- in particular, more mytharc movies, with William floating around in the ether ready to be reincorporated.

So, we must set aside this theory without resolution. How fitting.

THE RADICAL (OR CANONICAL) POSITION

There is a third train of thought: that William was both normal and abnormal. A creation of love, extra blessed with alien abilities. Not fated for a purpose-- born from a fluke of Fate (or perhaps in spite of it.) An example of "all things happen for a reason."

Perhaps this speculation is closest to the writers' true intent.

CONCLUSION

I believe Season 8 is a contained arc-- that there is enough evidence to prove William was a normal child born from Mulder and Scully's love. That Scully's fertility was restored by the very technology which robbed her of her ova nearly five years before. That her and Mulder's belief in the truth saved them from abductions and cancer and brain surgery-- and, more importantly, that their trust in each other guided them towards Millennium and Closure and all things.

Whether you believe in Je Souhaite's ending or Existence's extended edition or the Revival's final say, I think we can all agree that, at some point, William Mulder-Scully's arc strayed from its earliest intentions.

Thanks for reading~