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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
The X-Files
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.
  • Thanks to Carter's Failure Is the Only Option policy, plus the bugged office, that's all too plausible.
  • Mulder and Scully keep battling the monsters of the week — which are more of a threat to the Conspiracy than two fringe FBI agents.
  • Also consider that the Syndicate is a very small group. They simply don't have the man power to pursue leads when they are busy covering up a global conspiracy.

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.
  • That would be one hell of a comic.
    • Unfortunately, they made it into a lucrative CGI film instead. Happy days.
    • The fact that this concept has already been made into a super-great animated movie doesn't mean that it can't be made into an X-Files comic with a theme less serious than the show usually has.
    • Forgive me for tooting my own horn, but I've done this. This may or may not be what you were expecting. Click to enlarge the file.
  • All those leech men, vampires, werewolves, fear monsters, poltergeists, ghosts, cockroaches, voodoo priests, and pyrokinetics were supersoldiers expressly created by the conspiracy to fight the alien invasion.
    • And the Jinn?
      • Who do you think created them to begin with?
      • See the "Small Potatoes" theory below.
  • Alternatively: the monsters are naturally occurring phenomena made by the Earth in response to the alien presence. The aliens are like a disease, and all the other monsters are the planet's attempts at forming anti-bodies.
    • Mulder and Scully are pawns of the alien conspiracy because they get rid of monsters the way AIDS gets rid of antibodies.
    • Or Mulder & Scully are the antibodies, and the monsters were created to level them up to the point where they'd be ready to fight the aliens.
      • Three-faction war: Human military, monsters and supers, aliens. Five bucks says the space jerks are hosed.
  • Mulder and Scully will save us from the aliens. The mutants and supers will conveniently disappear when the aliens show up (except for Gibson Praise, since his powers are caused by active alien DNA).
  • Let's go all Batman vs. X on them. Aliens vs. the Tulpa (Arcadia) - Tulpa wins because the aliens wouldn't have a clue how to kill it. Aliens vs. the fire conjuring motherfucker (Fire) - fire conjuring motherfucker wins because he controls fire and burns the shit out of the aliens. Aliens vs. the insects (Darkness Falls) - insects win by... you get the idea.
    • Let's not forget the creepy voodoo hillbilly. If that stuff works, all you need are some alien dolls and microwave, and the problem is solved. And the "can imagine reality different guy" will lose all his contentment if the world ends via alien invasion and will imagine it all better. He'll be able to because he'll be miserable again.
  • Let's not forget all the natural disasters (fires, tornadoes, severe storms, blizzards, earthquakes, volcanoes, hurricanes, floods, droughts, etc.) that Earth suffers often... Unless the aliens come from a planet (or planets) that also have a large number of natural disasters occurring on a daily basis, they won't want to live on Earth until they perfect a method of controlling the climate. Maybe that's the reason for global warming: The aliens are trying to see if their climate control system works before they start terraforming Earth to their expectations! Since global warming causes more disasters in the short run, no one will guess the aliens' true purpose.
  • It doesn't matter who else fights against the aliens: John Munch exists in The X-Files Universe. Nothing can stand against John Munch. Not even the Evil Alien Colonists. Ancient alien conspiracy vs. Cranky Jewish Detective? Cranky Jewish Detective wins.
    • Munch will destroy the alien invasion with an army of Golems that he creates. Combined with a few guesses from above, this would make it Golems vs. Aliens vs. Monsters vs. Humans. Alternatively, Munch is a golem, and not jsut any-the First Golem.
  • The opening of "The Red and the Black" has the line "Twin wargods come to their father, seeking magic and weapons to eliminate the monsters of the world." While the opening of the preceding Patient X compares E.T.s with gods.

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.
  • She started as an agent of the Conspiracy, but didn't stay one. She was originally hired to keep an eye on "Spooky" Mulder but then decided to chum up with him; the two have been a team ever since. Since her rejecting her role as a spy was a huge plot point early in season one, it can't still be true for the rest of the show.
Which consperacy (there's a lot of shadowy yet exceedingly powerful organizations featured in the X-Files) is Scully an agent of? The Majestic Twelve, Millennium Group, and Syndicate are the largest three (known) conspiracies.
  • The Millennium Group, Scully's an FBI agent and Millennium controls the FBI.
  • The Majestic Twelve, MJ-12 investigates extraterrestrials - half of what's going on.
  • The Syndicate, who have been keeping an eye on Mulder for a long time.

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.
  • So he's Haruhi's FBI agent uncle?
    • Or Haruhi is his abducted sister.
  • So all the MOTW's are Tulpas?
  • But the show made clear that Mulder had no luck finding anything supernatural until Scully joined the X-Files. She, not he, is the magnet for the supernatural. Clearly, Kyon has a family member he doesn't know about in the FBI.
    • You could argue that Mulder's belief activated Scully's supernatural magnet. She's not shown to have a history with the supernatural before meeting Mulder (that was more her sister's thing, unless Melissa's new age beliefs were a reaction to Dana's supernatural magnet).
    • This might actually explain her skepticism as a defense mechanism. If your 6-year-old repeatedly sees the Jersey Devil in the back yard, she just has an over active imagination. If your repeatly 15-year-old sees the Jersey Devil in the backyard, she'd chalk it up to a cruel prank by her brothers or start repeating "it's not real" in her head. This might actually explain her relationship with her brother Bill a little...

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:
  • 1. All monsters were created by conspiracy scientists as slave and assassin/shock trooper labor for the aliens.
  • 2. All supers are prototypes for alien Human slaves (which was kinda confirmed in later episodes)
  • And 3. Now this one is tricky, How any outer dimensional supernatural forces (Ghosts, Demons, Angels, werewolves) or any other supernatural force would directly work or be enslaved by any extra-terrestrial force is kinda a hard one to explain. However it can be theorized like this:
    • the Aliens made a literal Deal with the Devil and have a entire army of monsters, demons, and the undead at their beckon call
    • God Is Evil and is helping the aliens just for kicks.
    • There is no God OR Devil and the aliens have allies from other Dimensions helping terrorize and subjugate Humanity.
However if anyone has any other theories about this please feel free to add.

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.
  • The parasitic slug creature the desert folk put in Scully in "Roadrunners" was a Goa'uld. They worshiped it like one.
    • Proof! Does that mean the Trust were the Syndicate?
  • This might apply to Scully's father as well, ie he faked his own death and took command of the Stargate program... Of course, this makes it either Hilarious in Hindsight or Fridge Brilliance. It also might also explain why Mulder and Scully seemed to have some measure of karma protection from the Syndicate.

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.
  • This is totally part of my fanon now.

Mash 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:

  • Paranormal activity: both shows frequently featured near-death experiences, one episode of M*A*S*H featured the disembodied, self-aware ghost of a dead soldier and suggested the existence of an afterlife. Father Mulcahy often pulls off miracles. And Klinger once ATE A JEEP. The 4077th is located in the Korean version of the Bermuda Triangle where the camp is unstuck in time, fluctuating between the fifties and the seventies, for eleven years throughout a two-year long war.

Conversely, Earth: Final Conflict and The 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.
  • That's a good theory. There are exceptions: Gibson Praise (active alien DNA), Flukeman (radiation), the polygamist with all the Demon babies (Satan, or a close friend thereof), Tony Shaloub's character (lab accident), the two girls in "Syzygy" (otherwise normal teenagers plagued by cosmic alignment), the metal dude from Doggett-era, the Great Mutato (backyard LEGO Genetics) and the parasitic twin (again, born before the 1950's), just to name a few with clearly defined origin stories. It's implied that humans are part alien; that's why Mulder and Scully kept running into various telepaths, telekinetics and psychics over the years. The Vampires in "Bad Blood" were implied to have been around before the 1950s. But yes, this still puts a lot of the Monster Of The Week episodes in context.
    • You forgot all the malevolent AIs that are running around, along with some of the animal episodes. There's also the Marine from "Sleepless", and the two soldiers from "The Walk" and "Unrequited".
      • And the Eves.

Las Vegas, Heroes, The X-Files, The Stand and Knight Rider all take place in the same universe.
Both Knight Rider and Heroes have a Montecito casino, the setting of Las Vegas. Linderman was apparently running the casino, which would fit with the Montecito's high owner-turnover ratio. It's possible that the Company was killing or "persuading" the previous owners, using people with powers, to get their hands on it.

Also, the Shanti virus, in an alternate universe, is what kills everyone in Stephen King's The Stand, except much earlier. (This is supported by King himself, who said that The Stand universe was just an alternate version of ours) — possibly due to time-travel or the Company experimenting with an early form of the virus. The Company coverups would also explain all the weird stuff that keeps happening to Mulder and Scully, especially if you've read the "Last One Standing" fanfic.

The "can imagine reality different guy" mentioned in the "Aliens vs...." guess is Haruhi Suzumiya.
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.
  • He could also be that guy from "Lathe of Heaven," meaning that the entire X-Files world is his dream. Or something.

The show is a documentary. Everything in it has happened or is happening.
Exactly What It Says on the Tin.
  • That would explain the "Cops" crossover episode.

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.
  • It's not really that he wants Mulder to develop a relationship so much as it is a quest for a sense of family. When Mulder confronts him in his apartment, he explicitly states that a family was a sacrifice he made for the cause, and implies that he is trying to prevent Mulder from doing the same. He delays revealing the truth about his relation to Mulder because he is trying to win him over (it's too late for Jeffrey, he would never love the man who tortured his mother) and finally feel familial love. Even one of the elders gets involved when Mulder is trapped on the train, because that's how important Mulder is to CSM. CSM just wants Mulder to understand and love him, and give up his dangerous obsession.
  • Interestingly enough, it's a common fan theory that "En Ami" is at least partly this. In the episode, CSM talks about wanting to leave a "legacy" for future generations and pesters Scully about her feelings for Mulder. He had definitely noticed how close they were. At some point in the episode, Scully is drugged (or, if you believe CSM, in an exhausted sleep). Now, he's already been shown to have the chip that cured Scully's cancer—why not one to fix her womb? Scully and Mulder begin their sexual relationship not soon after that, she becomes pregnant right away after being told by many a doctor she was barren. Tricky, CSM. Very tricky.

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.
  • Alternately, he was suspicious that she might be setting him up for a sexual harassment complaint and wasn't about to react in any way that could be used against him until he figured out what was going on.

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.
  • Key elements of the story never have to be shown (only hinted at)and when visual proof IS required,it is created and then quickly and "mysteriously" destroyed.
The purpose of the Ponzi scheme? To personally enrich the individual members of the conspiracy and give them access to power undreamed of in human history.

That is... until the events in the first film. THEN an alien group really DID try to takeover the Earth and the resulting panic and confusion exhibited the Conspiracy leadership lead to their own deaths.

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
Syndicateís 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 theyíre pulling the strings. Both groups know the other believes themselves dominate and both are assured itís part of the plan. In reality neither has an edge over the other.

The Millennium Group and the Syndicate arenít actually aware of each other
Itís possible that two different conspiracies spanning the government of the United States of America arenít 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.
  • The Marburg Virus would have killed all of the invading aliens, freeing Earth from extraterrestrial treat, in the process killing most of humanity. The Millennium Group inoculated themselves, planning to leave only those chosen by Millennium to rebuild.

Everything that happens after "Field Trip" is a hallucination.
They're still in that cave!

Thereís 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!
  • Wouldn't the name make more sense if there were TWELVE of them?

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 Agent Leroy 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.
  • Additionally, both shows take place in or around Washington, D.C.

The X-Files Division Becomes the Bureauís Mainstream. America Prepares for the Upcoming Colonization and People Kicks Aliensí Asses. Scully Becomes Head of the Bureau.

Having been forgiven the death sentence, having successfully cracked up the case (the one with the evil doctorsí operations in "I Want to Believe") and being a hero at the Bureau once again, Mulder decides to join the FBI again. AD Skinner reopens the X-Files and Mulder becomes its unit leader. He gets Agent Doggett and Agent Reyes on his team, plus some more up-and-coming promising young agents. Scully decides to give up her brilliant career in medicine yet again as well and becomes the X-Files lead science investigator. The team works mainly on the black oil vaccine. Scully retrieves some of the Well-Manicured Man research and being the medical genius she is, she develops a new and improved vaccine. The team has some trouble administering it as it must be kept secret so that the alien colonists would not get suspicious. People are now seriously Properly Paranoid and do not know what to make out of it, but the Army and CIA are preparing for the invasion, collaborating with other state governments and their secret agencies. Mulder is torn as he wants to be telling people the truth, yet he wants to be able to save them. The team's lab also creates and tests weapons using that metal which is the aliensí kryptonite. The strong vaccine starts reversing the process with Billy Miles-like alien pre-settlers. They find a top secret research facility with children whose parents were abductees. One boy looks suspiciously similar to a photo of six-years-old Mulder. Yeah, you know who he is. William was abducted from the Van de Kampsí and taken to be tested by the alien conspiracy and the colonists, but his motherís vaccine is not even necessary because he was immune to the virus from the start. On top of that, while investigating, they also find Mulderís sister. It turns out the recent tissue from "Paper Clip" was real and Cassandra Spender was right. It was the take-in by the fairies/angels that was fake and Red Herring! When the aliens come at last, they are horrified to find out that not only are their allies useless, but they cannot use humans to host their bodies to fully develop any more. And in addition, people kick their butts and destroy them completely (or force them to return to their new planets). Scully then becomes head of the Bureau as Mulder predicted in "Squeeze". She even skips AD position and section chief position because she's that good. The Mulders are now a fairly happy family, save for some moments when Bill Scully pesters Dana that she should have never given up William in the first place and that she should have stayed practising medicine.

Sheriff John Oakes, ex-marine Denny Markham, Detective Manners and PD Captain Jack Bonsaint are quadruplets separated at birth.

Instead of being just a strange case of You Look Familiar, Sheriff John Oakes from "Die Hand Die Verletzt", Detective "Bleeping" Manners from "Jose Chung's From Outer Space", ex-marine Denny Markham from "Unrequited", and Police Department Captain Jack Bonsaint from "Chinga" are actually quadruplets who were Separated at Birth. Exhibit A: They look identical. Exhibit B: They made similar career choices (three times the police force and once the military) which is a phenomenon often observed with those cases. Exhibit C: At least two of them were named John by their adoptive parents, Jack being a domestic variant of the name. Again, it has been observed in cases with siblings separated at birth. Exhibit D: Their DNA must draw mysteries and unexplained phenomena.

The mysterious enzyme from El Mundo Gira is actually Fightin' Juice.
The meteor that brought it to Earth was an Ork Rok that broke up on entry due to the Orkz' notoriously haphazard style of piloting, spilling its cargo of Fightin' Juice all over the migrant camp. Fightin' Juice is an alien elixir that enhances the growth of fungus, just like the stuff in the show. As to why the Buente brothers absorbed it, it may be a result of genes passed down from the C'Tan and their enslaved Necrons' experiments on Earth during the War in Heaven, as they had been looking to create a new Super Soldier race to counter the Old Ones' Orkz and Eldar.

The Show takes place in the same universe as Highlander.
Scully is a immortal that hasn't had her gift awakened yet, thus explaining the hints dropped about her never dying or having a long life.

Mulder won't die from autoerotic asphyxiation.
Clyde Bruckman was talking about himself. Those weren't sleeping pills he was using when he put the bag over his head, it was Viagra!

The Greys ultimately win, which begins the series of Falling Skies
Ultimately, Mulder and Scully fail to prevent the aliens' invasion of Earth. The aliens dispose of the Syndicate and perfect the human/alien hybridization process by using the harnesses that turns humans into Skitters. This is hinted in the first movie, as Mulder, miserable and drunk, makes a scene at the bar, shouting, "The sky is falling and when it hits, it's going to be the shitstorm of all time."

Samantha Mulder never existed
Mulder just thinks he has a sister who was kidnapped as a kid. That person never existed. She's just a successful product of brainwashing and hypnosis.

The time loop in "Monday" was caused by Scully's immortality
The hints about Scully's immortality had already been dropped in such episodes as "Clyde Bruckman's Final Repose" and "Tithonus". In "Monday", it is implied that the time loop was caused by some sort of chink in the universe, something that should not have happened, such as Scully dying in the bank robbery when Death is never supposed to come for her. Therefore, that Monday repeated itself until it could solve the paradox of Scully's death.

The titular X-Files were the successor to Blue Rose Cases...
As the conspiracy to colonize earth began to pick up, the incidence of supernaturally inclined unsolved cases being referred to the FBI increased dramatically. The Blue Rose protocol was far more secure, allowing agents to perform incredibly sensitive work on long term with minimal exposure of what was going on, but was also incredibly inefficient. The X-Files were a far more efficient, but far less secure, method of allowing the FBI to investigate suspicious and potentially paranormal cases. However, this came at a price, and eventually lead to the abandonment of the X-Files due to the machinations of the Conspiracy...
  • Denise Bryson was either yet another wrinkle in the tapestry of Mulder's complex biography and sexual identity, or possibly a secret twin/clone sibling with an origin wrapped up in the Conspiracy.
  • Likewise, the Briggs and the Scullys were related families in some way. Both patriarchs looking identical and having similar careers in the military can't just be a coincidence, can it?

... and the predecessor to Fringe Division.
... at least until a new, more powerful agency arose in the federal government: Homeland Security. With a new investigative body at work in the US government, new resources could be directed to cases that would formerly have fallen under the purview of the X-Files. And when an organization of super scientists began demonstrating mad science on a massively public scale in anticipation of a global war with another world, Homeland Security was forced to set up a joint task force with the FBI in the form of Fringe Division. Though their work is also secretive, the combination of a much higher profile and nearly limitless resources mean Fringe Division is much harder for the Conspiracy to control. Logically, this would disrupt or even delay the colonization plan (which is good, since the Aliens would have had to fight the Observers for control of Earth, alongside all the other monsters of the week).
  • This one is actually implied in Fringe, when Agent Broyles is Hauled Before A Senate Subcommittee to defend Fringe Division's use of resources. The "failure of the X-designation" is called out as reason for skepticism in Fringe Division's capabilities.


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