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The Colonization will be a Great Offscreen War.
Given the fact that any sort of movie attempt in time for December 2012 would have had to have gotten started by now, expect any third movie to be like "Yeah, remember how we stopped that Alien Invasion? Those were the days, now excuse us, we need to go stop the Monster of the Week."
Mulder and Scully are more of an asset than a threat to the Conspiracy.
They suck at stealth, have no concept of burden of proof, wouldn't know what to do with evidence of aliens if it were handed to them on a silver platter, and rarely follow up leads. On the other hand, leaks in the Conspiracy can't help but seek them out. Since these two often discuss these elements in their known-to-be-bugged office, the Conspiracy hears all about it and can patch their system.
The alien invasion was canceled after they briefly landed and were torn apart by all the other monsters.
With leech men, vampires, werewolves, fear monsters, poltergeists, ghosts, cockroach men, and voodoo priests running around the world in great numbers, the aliens don't have a chance against Earth's homegrown monsters.
Scully is an agent of the Conspiracy.
Her purpose is to keep a close eye on Mulder and prevent him from getting anywhere near the real issues at stake. She also serves as a useful distraction and directs his attention towards the small, irrelevant issues. This explains her constant skepticism to the point of illogicality - it only encourages Mulder to delve further into the things that don't really matter.
Mulder's belief is so strong, it warps reality.
All the monsters and weird things he goes to investigate don't become real until he starts to believe in them.
The Monster of the Week episodes are connected to the Mytharc.
The monsters are all alien creations set loose on Earth to distract Mulder & Scully from the aliens' real plans.
To boot many fans considered the final "Truth is Reveled" episodes to be somewhat of a Ass Pull to make a story thread so interwoven and complex (partially due because of the random paranormal elements) for seven whole years that the final answer of a (while somewhat Foregone concluded) somewhat standard alien invasion (with kind of while realistic still generic looking aliens to boot) seemed kind of generic and somewhat cookie cutter for such a great series.
So this tropers WMG is that contrary to the above theories literally ALL of the spiritually, superpowered, and monsterous paranormal elements are connected and actively working for the conspiracy. Technically all this can be proven by one simple trope. Mulder believed at first that all these creatures were connected by or to the conspiracy in some shape or form and since the All Theories Are True trope was in full effect on this show it probably was true.
Basically this WMG can be broken down like this:
Skinner survived the series finale by going undercover in the Stargate program.
He had to survive the series finale to show up in the second movie. So, maybe the aliens/conspiracy people awaiting him in his office at the end of the series weren't the evil murderous sort, but rather benign conspirators from Stargate Command who wanted to recruit him. He went on to become a spaceship captain for a short while before returning to his job at the FBI, possibly to assist with covering up the Stargate program.
Babylon 5 is the future of The X-Files.
Bureau 13 and the Psi Corps are the descendants of supersoldiers and other elements of the Conspiracy. Once they got jump gates, Earth threatened to blackmail the Vree, which is why the Greys have cooled down (except for the Streib, but they're a different faction). The Vree and the Streib are in fact the descendants of the colonists and the alien rebels. In the 23rd century, the conspiracy put President Clark in power because they appreciated his anti-alien sentiments.
M*A*S*H and The X-Files are set in the same continuity, and either Bill Mulder or the CSM was Major Flagg (Ed Winter's character) from M*A*S*H
This theory depends on how much of the Cigarette Smoking Man's back story (as shown in "Musings of a CSM") we accept. The theory depends on the similar characteristics and back stories of X-Files characters Bill Mulder and the Cigarette Smoking Man (CSM) and M*A*S*H's Colonel Flagg. Bill Mulder was an agent of the Cigarette Smoking Man who worked with the Conspiracy. If we accept CSM's early back story from "Musings," we also have the fact that both CSM and Bill Mulder knew each other when they served in the Army in the late fifties/early sixties. Earlier in his career as a Man in Black, Bill Mulder had hunted communists in the State Department. Flagg was a mysterious military Man in Black who impersonated other officers, carried out secretive and sometimes self-contradictory missions, spoke in hyperbole and threats, and was obsessed with hunting communists. He came with loads of fake IDs, so we can safely guess that Flagg wasn't his real name. It was either (Bill) Mulder or the nameless CSM.
Also, it is common knowledge that M*A*S*H and The X-Files take place in the same universe.
Further similarities between the X-Files and M*A*S*H include:
Conversely, Earth: Final Conflict and X-files are the same universe.
The "Colonists" were the Taelons. Think on it. the Taelons have fertility issues and need to make human/Taelon hybrids in order to survive. They also need cannon fodder in their war with Jaridians, laborers to grow them food, etc. They operate with a nominal hive-mind and wouldn't have much of an issue with what we see in Herrenvolk. Their agents are also given implants, both to enhance their physical capabilities and to track them. These implants break down, the humans die. One of the first symptoms of these breakdowns are nosebleeds - just like Scully had when her implant was removed.
This would leave the flame-throwers as Jaridians. They have super-short lifespans and are out to sabotage the Taelons. They're also pretty vicious with their methods. The "Kindred" from "Genderbender" have much the same MO as Ha'Gel - shapeshifting, a touch that takes over their intended "mate," and human "mates" literally dying from endorphine overload. Earth is their last refuge after the Taelons and Jardians have decided to hunt them down.
Now, cap that off with the Magnificent Bastard of the series, Ron Sandoval. He's cheerfully working every side in this mess to his own advantage. And before he got appointed to the Taelon embassy, he was an FBI Agent, specifically an infiltration expert. Now, run this scenario: After Mulder and Scully were disgraced, he's a young agent saddled with the X-files. He infiltrates the Syndicate and pretty much takes CSM's position while Joanathan Doors buys out Strunghold's assets. The pair of them vie for control. The Taelons, in the meantime, have had enough of Plan A wrecked by Mulder & Scully that they have to resort to Plan B and look like benevolent visitors while carrying on under the radar. Doors decides to be overt about the fight and found the Resistance, while Sandoval does what he does best in infiltration. The Motivational Impariative in his implant slows him down a bit, but when Ha'Gel shorts it out, he's right back at the sabotage game.
The Father of the Guy from Small Potatoes is the source of most of the mutants.
You know, the father of the shapeshifting mutant freak who was knocking up all the women in town and giving them tailed babies. His father was like that, but even more prolific - he's the father of most of the mutants born after the 1950s whom we've seen on the show. And maybe his father was Eugine Victor Tooms.
The "can imagine reality different guy" mentioned in the "Aliens vs...." guess is Suzumiya Haruhi.
He's got Haruhi's powers; that's more than enough logic by WMG standards. There are a couple of different reality warpers, but the likelihood that any given character is Haruhi is directly proportional to the number of times they appear on a WMG page.
The show is a documentary. Everything in it has happened or is happening.
Exactly What It Says on the Tin.
The reason CSM never became a published author was not because of karma.
If you look, you'll see that Jack Colquit is a blatant Marty Stu character. The publishers didn't want such a story on the shelves, so they consistently turned CSM down. The skin mag was just the low rung the companies thought it deserved.
After the first half-season or season, Scully was only the Agent Scully as an in-universe balance for Mulder.
Because if she hadn't, and he was still right all the time, she(thinks she)'d eventually be going along with him kicking down the door of a random pizza guy's house and shooting him with an automatic stake launcher after spending their travel budget for the case on garlic oil and bags of aniseed. Mulder doesn't really believe Despite Aliens, No Jesus, he just believes in Space Jesus and a Sufficiently Advanced Alien that probably doesn't bother with miracles any more, and acts as the Agent Scully in order to keep Scully herself from getting out of hand or (quite likely, but not necessarily the sole reason) to give her grief over her for her Arbitrary Skepticism.
The main reason Scully was assigned to the X Files was because Cancerman just wanted his son to get laid.
It wasn't because she was scientific and skeptical, it was because she was single and hot. We see him spying on their first meeting. He also goes to great lengths to keep them together, including getting her returned after her abduction, and giving Mulder the cure for her cancer. In the episode 'En Ami' he even tries to convince Scully to admit she's in love with Mulder. Face it, the Cigarette Smoking Man is the biggest Mulder/Scully shipper.
The aliens from Genderbender are from the same planet as the Shimeru Clan.
Obvious, really.
Mulder has some kind of affective disorder.
In Pilot, Scully comes in in a robe and asks Mulder to look at something (the marks on her back). He doesn't react in the slightest to a woman disrobing in front of him. Not even with a surprised "Hey, wait a...". Unless he's gay, it's hard to imagine he'd be so unaffected.
The entire Mytharc (not the stand alone episodes) is a gigantic Ponzi scam being perpetrated by the Conspiracy...until the events of the first X-Files movie.
The Millennium Group was manipulating the Syndicate from the beginning
As an Ancient Conspiracy Millennium already had sufficient influence when the Syndicate formed, enough to subvert those alien collaborating upstarts.
The Syndicate was manipulating the Millennium Group from the beginning
Syndicate’s unique advantages allowed them to infiltrate the Millennium Group, what defense could those conspiring old men field against *that*?
The Millennium Group and the Syndicate *thought* they were manipulating each other
Syndicate and Millennium have infiltrated each other so thoroughly they both believe they’re pulling the strings. Both groups know the other believes themselves dominate and both are assured it’s part of the plan. In reality neither has an edge over the other.
The Millennium Group and the Syndicate aren’t actually aware of each other
It’s possible that two different conspiracies spanning the government of the United States of America aren’t actually aware of each other.
The apocalypse the Millennium Group were preparing for was the impending alien invasion.
If the invasion was ever shown, there would be biblical references tied to the Book of Revelation in the pattern of destruction, and all the religious figures of the Judeo-Christian tradition seen in the show would rise up to fight the forces of darkness. So... If Aliens Than Jesus.
Everything that happens after Field Trip is a hallucination.
They're still in that cave!
There’s only a handful Majestic Twelve agents.
For a super secret agency tasked with protecting America from extraterrestrials the Majestic Twelve never seem to field more than three agents at a time, this is because there are only eight agents!
The events of "Musings of a Cigarette Smoking Man" are the next Jack Colquitt story that CSM wrote after "Take A Chance".
The details are wrong because he realized that Frohike read the first story and came up with details about him that were a little too close for comfort.
Also, CSM realized that if Frohike was reading Roman a Clef (heh), then other conspiracy nuts were as well - and that it was a great way to spread disinformation. The magazine was subsequently taken over by one of his many shell companies, and revamped to cater specifically to that market.
Melissa Scully survived her gunshot wound and changed her name to avoid any future attempts on her life.
..as Diane Lastnamehere before marrying NCIS Agent Jethro Gibbs, divorcing him, marrying FBI Agent Fornell, divorcing him, then ... you get the idea. Considering the character (Melissa) was originally conceived as a love interest for Mulder, one can assume she has a thing for law enforcement officers.
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