I agree that Mulder and Scully did a lot of foundational work to make the Hollywood Nerd and women in STEM subjects more mainstream and no other show did as much for prioritizing male intellect over athleticism and female aptitude over allure. Mulder and Scully were presented as an image of male and female professionalism. The unfortunate reality of the show, however, presented them as deeply unprofessional.
While I am not a fan of THE X-FILES, I do understand THE X-FILES and I feel I can say: the mythology mostly made sense until Season 10.
I would say that about 85 per cent of Seasons 1 - 9 made sense, and the 15 per cent or so that didn't make sense is pretty reasonable as no story is without human error.
Reputation over Reality
THE X-FILES certainly had a *reputation* for having a nonsensical mythology that was made up as the show went along, but having watched the whole series when it first marathoned on the Canadian SPACE channel, I didn't find that to be the case.
Reviewers and viewers who described the mythology as confusing or contradictory in Seasons 1- 9 always struck me as extremely *casual* fans who maybe watched one out of four episodes. The mythology was very, very straightforward.
The original inhabitant of planet Earth was an alien being called Purity that manifested in two forms: gray aliens and the black oil virus. To survive the Ice Age, Purity departed from Earth but remnants of the intelligent black oil virus were left behind. Purity and their black oil virus conquered the majority of life in the universe, infecting all life forms via the black oil virus, and then returned to Earth as Colonists, intending to use Earth as a breeding ground.
Before the invasion could begin, one of the Colonist ships crashed to Roswell in 1947, alerting world shadow governments to the threat. The shadow government, the Syndicate, threatened to trigger nuclear winter unless the Colonists withdrew; the Colonists in turn threatened to exterminate the planet. A bargain was struck: the shadow government would be permitted to survive and choose survivors if they facilitated the Colonists' invasion of Earth to use black-oil-possessed humans as a slave race.
Resist or Serve
However, both sides were plotting treachery: the Colonists intended to use the infected humans as breeders regardless of the deal. The shadow Syndicate was attempting to create a vaccine against the black oil. A third faction entered the conflict: the Faceless Rebels, a race of aliens who had sealed their mouths and eyes shut to prevent black oil infection and landed on Earth and killed most of the Syndicate members.
The Colonists replaced their human collaborators by capturing key members of world governments (and a small town sheriff and some of his neighbours, very odd). They converted these humans into alien supersoldiers to infiltrate all levels of human society to keep their 2012 invasion plan on track. The series ended/paused in 2000 with a two part finale that gave a full summary of the mythology, the intent being to continue/conclude this story in a feature film series that didn't come to pass.
There are a few myth-arc elements that don't fit into the overall story very smoothly. Episodes in Seasons 3 - 4 indicate that the aliens are quietly infiltrating the human race, living civilian lives, waiting for humanity to destroy itself so that they will quietly inherit the planet. This doesn't track with later seasons indicating that the plan is in fact outright invasion.
The alien-human hybrids were intially presented as the civilian-aliens experimenting with alien-human co-existence and being exterminated by the alien bounty hunter at the behest of the Colonists. The bounty hunter, however, would later be shown as aligned with the Faceless Rebels.
I don't understand what the bees were all about and nobody has ever been able to explain it to my satisfaction.
It's unclear why the Colonists wanted a few randoms from a small American town to be their supersoldiers when the other supersoldiers were high level government operatives. But this is well within the range of human error for most shows with myth-arcs.
Most of the other aspects of the mythos fit into Colonization: the clones were attempts to create black-oil-resistant biology, the abductions were for tests for the same project.
The Season 10 premiere, however, abruptly declared that the entire Colonist plotline had been a massive hoax and that the true endgame had been humans using stolen alien technology to create the Spartan Virus to massively depopulate the human race.
This did not track with the Colonization arc at all. While an understandable retcon to simplify things, the Season 10 finale made it even more tangled by declaring the Spartan Virus and Colonization to be the same conspiracy and presenting the Colonization conspirators as participants of the Spartan Virus plot.
This threw Seasons 1 - 9 into a state of hopeless confusion: how had the 2012 invasion date and the abductions and the black oil been relevant to a plot about human depopulation? And what about the supersoliders?
This is the part where THE X-FILES actually stopped making any kind of sense in its mythology, sadly. Carter was shockingly careless and indifferent to a mythology he'd built up over nine seasons. Season 11's premiere confusingly declares that there was a plot for alien colonization but it's not clear if this is a reference to the Spartan Virus or the disavowed Colonization plot.
To Be Fair
With THE X-FILES having been off the air between 2000 and 2016 and having missed the 2012 invasion date, it made sense to set the Colonization arc aside. But Carter didn't conclude it; he come up with a completely different story for Season 10 and claimed it was the same story as Seasons 1 - 9.
It seriously undermines the entire structure of the show. It makes Mulder look ridiculous for devoting 1993 - 2000 (if not more) investigating an alien invasion plot that was all a joke. In Season 11, Mulder encounters Deep Throat's grave, but Deep Throat's death and role in the Colonization conspiracy has been completely undermined by Colonization being a hoax. All the angst over hiding William from the Colonists is silly if the Colonists weren't real and had no plans to invade.
The X-Files Reborn
I think that Carter could have wrapped up the myth-arc in a single episode for the Season 10 premiere. The 2016 premiere could have shown an uninvaded Earth, Mulder and Scully retired from the FBI -- only to be recalled due to a series of murders where the victims turn out to be former employees of the now-defunct Syndicate. The murderer turns out to be a man targeting people he deems to be traitors to the human race in an alien invasion.
Mulder confronts the murderer, tracking him to the New York City Syndicate headquarters. Surrounded by artifacts and tools of the Colonists, Mulder reveals to the killer: the Colonization of Earth has been cancelled. The Colonists have lost interest in Earth, a warming planet with depleted resources, and no invasion is coming. The murderer can't accept that Colonization has been cancelled as the conspiracy gives his life meaning and kills himself.
At the end of the episode, Mulder and Scully prepare to return to civilian life only to find that since 2000, the X-Files office has accumulated thousands of paranormal casefiles, all unsolved, all filed under X, all in need of a believer and a skeptic to investigate. Mulder and Scully decide to return to the FBI and the adventure begins again... preferably with Glen Morgan running the show...
I have sent the webmaster of EatTheCorn.com a message. I've asked him what the bees were all about.