I’m not really up on all the twists and turns the show has had over the years. Could someone give a quick summary on the major events of the mythology and where it stands now? Have they ever answered if we are alone or not in the show?
Yes Aliens exist, Scully’s son has alien DNA. She gave him up at birth so bad people like the Smoking Man would not find him.
In the newest version Scully was having visions of him so her and Mulder were trying to find him. The bad people were also trying to find him.
He is a teen now and he has a power that he can make people see him as another person. At one point he was at a gas station filling up and so was scully and she talked to him briefly but she saw him as someone other than her son. Then he drove away.
To expand on that Roswell was real, we made deals with aliens to let them experiment on us in exchange for technology, and Smoking Man has a self-righteous plan to kill everyone in the world except those who have an antidote/alien DNA. I’m not quite clear on that or why.
The mythology got very convoluted over the course of the show, and the revival made it even more convoluted, but my understanding is that the latest version in the revival is that the supposed deal with the Grays and the “black oil alien” conflict were simply more layers of disinformation. The Conspiracy is (I think) entirely human, and uses weird technology to perform experiments for its own ends, which are murky at best. I think at least some of the technology the Conspiracy uses is supposed to be captured alien technology, but I think even that is supposed to be uncertain, even to Mulder and Scully.
Their son does have “alien” DNA, but I think (this seemed very convoluted and murky to me) there is still supposed to be some ambiguity within the show about whether his engineered DNA is actually extraterrestrial, or purely human experimentation with artificial DNA.
Actually, fairly early in the show’s run, the third season episode “Jose Chung’s From Outer Space” featured a plot with multiple unreliable narrators, and at least one of the narratives featured U.S. Air Force personnel, disguised as Grays, flying an “alien” craft, and abducting random U.S. citizens, in order to…do something. Entirely unclear what the goal was. This plot point actually perfectly fits in with the revival’s plot that “alien abductions” are actually Conspiracy operations using Grays and UFOs as cover.
Depends on what time in the series run you are asking about.
In the original series, prior to the “super soldiers” arc, the facts were:
Aliens landed
CSM and Mulder’s father were there
Mulder’s sister and several other children were given as hostages to the aliens
The rest is less clear:
Aliens were going to take over our planet
Probably using the “black oil”
The group which became The Syndicate made a deal with the aliens - delay takeover and allow us to work on getting things ready, in exchange for being spared
The aliens in charge of the takeover were not necessarily the aliens we see. Those may have been captured/slaves/hybrids. The real aliens may or may not be humanoid, or even solid.
An alien/human hybrid may or may not have been part of the arrangement, or may have been a side project
Getting ready also involved installing some alien virus thing in everyone via the smallpox vaccination. And bees. And corn.
Despite the delay arranged from the original meeting, the day of takeover approached, And passed. The takeover was supposed to be 1997?. When that passed, and the show runners wanted to continue, they just decided to completely ignore the alien takeover and switched to a secret government plan to make genetically-altered (with alien DNA? who knows!) super soldiers. Then the show became about Mulder (and later Doggett) dealing with them. Nothing ever came from that, either.
In the new series…your guess is as good as anyone’s. Obviously Scully’s notAlien!Miracle Baby is in fact part alien. But where the alien part comes from wasn’t clear before I gave up.
Things not clear in any mytharc:
Is the smallpox scar part of the alien takeover, or part of the resistance to the takeover?
Does cutting off the arms of resistance people really do anything?
Is the Black Oil a tool for alien takeover, or is it actual aliens?
What about the BEES?
Are they Syndicate traitors, or heroes, doing their part to stop the alien invasion?
Are Super soldiers part of the alien invasion plan, or a response to the aliens - a weapon to defeat them? Or did the show runners just not care?
What do the “alien hit men” with the ice picks mean? Are they tools of the invaders, or resistance fighter?
Who are the alien resistance with the sewed up body orifices?
Why are aliens putting small tracking/monitoring thingies in the necks of abductees? Are these the invasion aliens?
Outside of the mytharc:
Are the gender changing vampire aliens part of the invasion, or just another species that like our planeet?
Are the aliens that prevent space launches part of the invasion?
Are vampires vulnerable to the Black oil?
Did the alien spacecraft tech come from the invading aliens or someone else?
Why are aliens still abducting people despite the invasion already underway?
Who or what are the alien bounty hunters?
Which aliens are sending robot cockroaches to spy on us?
If the aliens are taking over, why is the government experimenting on people and making them killers, or keeping a top secret lid onpeople whose shadow can kill?
Why is The Syndicate still killing aliens that land under international sanction? Are these the invading aliens, or other aliens?
And, the biggest mytharc question:
Why is there an X-Files department? It runs counter to everything The Syndicate wants.
I see gdave’s post came in while I was writing mine.
If that’s the “truth” (that there never was an alien invasion, and everything is conspiracy mongering) that doesn’t fit any better. The show is still full of contradictions. There ARE several species of alens out there (actually, HERE).
Jose Chung is an interesting episode. I had never thought to use it as a clue to the show. I always accepted it as showing how everyone has incomplete information, and that it might be impossible to know what is going on. That it might show the “truth” about the mytharc is fascinating.
But does that mean Lord Kimbote is real?
Just consider the show a sci-fi conspiracy thriller version of Gilligan’s Island with The Smoking Man as The Professor and it all makes more sense. Or, at least as much sense as Gilligan’s Island, which is to say, none at all.
Stranger
Ha!
I’m thinking more like the series La Femme Nikita. In that show, you have this all-powerful agency dealing with “terrorists”, and this other all-powerful “terrorist” organization. The terrorists never seem to actually terrorize anyone, or even have an actual goal, but they sure seemed to have a lot of funding. And the secret agency never seemed to be able to finish them off.
All they seem to do is go at each other like Spy vs Spy. And so the circle goes round and round.
In The X-files, The Syndicate does horrible experiments on people with apparently no end game in mind. They don’t appear to be working towards anything. Torturing people for fun is enough for some, but unless you’re a zealot, you want to get paid, too. And they aren’t making gazillions of dollars doing it. But the folk working against them seem to be working against the “fake” goal (alien invasion). Wouldn’t the resistance eventually figure out what was really going on?
This show really makes me angry. 
I think I’ll just stick to watching the non-mytharc episodes.
Prior to the change to super soldiers, I had a nice theory that fit the stories and made reasonable sense. In my theory, the Syndicate are actually the good guys. They lied to the aliens, and had been working against them from the beginning, That’s what the X-files was for - to find weapons to defeat the aliens.
An army of people whose shadow can vaporize people would be a formidable army. Insects that wrap you in cocoons, people that can deform themselves, that can live forever, telekenetics, firestarters, mind controllers, weather controllers, demons, alien tech craft, advanced AI, vampires, a way to trigger killing rage in the populace - these all might be used to defeat an invasion force.
I wish they’d used that.
Fox couldn’t afford to hire Patrick Stewart, Hugh Jackman, and Famke Janssen for a weekly series.
Stranger
An alien spacecraft takes off from the beach of a Pacific island, just as a crew of castaways comes running out of the jungle.
Mulder: Wait! Wait! Don’t leave!
Skinner: <takes off FBI cap and hits Mulder with it> Mulder! Your wacky schemes made us miss ANOTHER spaceship!
Scully, inexplicably wearing an evening gown: Eh, I’ve seen better special effects.
Why the hell can the Professor make a nuclear reactor out of a coconut, but can’t fix a hole in the Minnow?
Just where did Thurston Howell III get all that money?
Ginger or Mary Anne?
The truth is out there…
My understanding is that, in the revival, the show is trying to be deliberately ambiguous about that. The Syndicate is faking at least some UFOs and alien activity, for ambiguous reasons, but there may also be real alien activity on Earth. For that matter, the “fake” UFOs and alien tech the Syndicate uses may actual be real, captured UFOs and alien tech, or may be entirely human-engineered black budget super-tech, or a mix of those.
I think that the “truth” of the mytharc is precisely this - no one really knows what’s going on. The Syndicate has secrets wrapped in mysteries wrapped in enigmas, and plans within plans within plans, but even at the highest level, there’s still stuff going on that even the Syndicate doesn’t really understand. The world is just a really weird place. High Strangeness rules. Imho, it’s only at this level that the X-Files mytharc works at all, and for this reading, “Jose Chung’s From Outer Space” and “Mulder and Scully Meet the Were-Monster” are the two seminal episodes.
More prosaically, as is almost universally true with “puzzle-box” shows, I think Chris Carter is flailing at trying to put together a coherent “mytharc” for a show that’s lasted for 11+ seasons, with dozens of writers and directors contributing their own visions, and the result is an incoherent, shifting mess.
Who can say? 
The X file Men
My personal theory (in the early years when I thought there might actually be a coherent plot line) was kind of the opposite of that. My theory was that the Conspiracy was using Mulder as a stalking horse to root out and neutralize weird wild cards that could interfere with an alien invasion. That was why They allowed the X-Files division to exist - it was actually serving Their purposes. However, there may have been disagreement among Them as to whether the benefits outweighed the risk to Their own plans. So attempts to undermine and close the X-Files were either double-fakes to manipulate Mulder and Scully and keep them “on-mission”, or a result of internecine feuds within the Conspiracy, or some combination thereof.
I like that one. It fits, too.
I think there was a consistent backstory to some epsisodes, but later Chris Carter was just throwing stuff out there. I always preferred the “monster of the week” shows.
I too.
Just one question: why would a retractable ice pick be such a big deal?
Vince Gilligan’s Island.