In "The Jersey Devil", Mulder argues that the creature he saw can't be human because no human could've gotten up to the rooftop that fast. The fact that the previous freak-of-the-week, Victor Tooms, scaled a brick wall bare-handed only lent credence to his assumption for the audience. But the autopsy done on the female's remains suggests she's a normal, albeit feral, human. Which suggests that she was on the rooftop all along, keeping lookout, while her child crept up to raid the dumpster. When she spotted Mulder down below and/or the cars approaching the alley, she risked standing up to distract Fox's attention so her offspring could safely retreat from the area. Whatever the heck she actually was, she wasn't a bad mother.
In "Audrey" Mulder wonders if he likes sunflower seeds because his father likes them, thus making it genetic. Scully argues that no one is born liking them, it's all a combination of nurture. Mulder recounts that he would wake up, afraid to be the only person on earth, but he could hear his father eating sunflower seeds, which would calm him down. The environmental factor influencing Mulder’s love for the seeds was the feeling on contentment after hearing his father eating them.
An all-powerful evil conspiracy... could not oust rogue Agent Mulder and sympathetic Assistant Director Skinner from the FBI, or at least remove them to some insignificant bureaucratic duty? Explained (rather poorly) by the back story of Mulder having been regarded as a hero who aided in the capture of a vicious serial killer early in his career, and therefore any action against him would be a public relations pain in the backside. Not explained by the fact the Evil Conspiracy had already ousted people far more important and powerful.
Mulder was the Smoking Man's son, and he sacrificed his wife and Samantha to the aliens to protect Mulder. Krycek and the Well-Manicured Man were protecting him as well.
I always thought it was because no-one liked or believed Mulder; this way, anything he actually found out was guaranteed to be treated as a Cassandra Truth. In a way, Mulder was an extra layer of protection.
The conspirators may also have found him a convenient stalking horse, when investigating strange events that they weren't involved in. All those Monsters of the Week, for example.
Take it even further, actually: the Cigarette-Smoking Man always paid close attention to wherever and whatever Mulder went and did, and there are several hints throughout the series that, when it didn't interfere with their specific projects, the "cabal" had no problems implementing whatever safety procedure suggestions he would make regarding dangerous unexplained phenomena. To put it another way, Mulder was half a whistle-blower, half SCP agent. They would've been fools to have actually gotten rid of him completely, and they knew it.
It was likely a useless move. Mulder has shown that it doesn't matter if he is in the FBI or not — he'll go after the truth with or without their help.
He also had a few friends in high places himself at times.
It kind of zigzags. The Syndicate was mostly concerned with drawing undue attention to their plans. They couldn't let Mulder succeed, but if they killed him, it would just "turn [a] struggle into a crusade"; call attention to the project and give credibility to his beliefs, spurring further efforts to uncover the truth. They may have had a good reason for it, and not just selfishly... (see below)
"The Unnatural": The end scene has an aspect of Fridge Brilliance to it. Mulder uses the Hands-On Approach to teach Scully how to play baseball. The entire scene is based on Scully telling Mulder she'd never hit a baseball before, instead finding better things to do than "slap a piece of horsehide with a stick." This is most likely a lie. Scully was introduced as someone who defied female stereotypes and enjoyed being One of the Boys. Her mother tells Mulder in season two that she was a tomboy, unlike her sister. She got along well with her brothers, who gave her a BB gun for her birthday and showed her how to use it. Moreover, she was very close with her father and spent a great deal of time with him. The chances of her never hitting a baseball are pretty slim. But judging by the look on her face, she didn't mind being taught one bit.
"Arcadia:" Mulder and Scully go Undercover as Lovers to solve a case. Mulder mentions this is their first case since being back on the X-Files, but complains that it isn't an X-File at all. And he's right; though the case turned out to have paranormal elements to it, it was originally just a missing persons case in a seemingly perfect neighborhood. Which means that out of all the male/female partnerships in the FBI, whoever was in charge of the case thought that Mulder and Scully would be the most believable as a married couple.
That person was Skinner! Who seems to be the biggest Mulder and Scully shipper in the entire FBI. Asides from risking his neck to save them and being the only person to witness Mulder and Scully kiss. Asides from this assignment he also gave Scully that Bureau credit card to "enjoy their night on Hollywood". He misses his ship so hard that he tried to recreate them with Einstein and Miller.
The title of "Red Museum". Largely meaningless in the context of the episode - but on a meta-level, it's a collection red herrings. Enough to fill a museum perhaps...
It's not meaningless; the "control group" in the episode is a religious group who call themselves the Church of the Red Museum. Mulder even asks the significance of the name. The leader took his congregation to cattle country and bought a ranch, turning "500 head of cattle into pets." The leader called it a "monument to barbarism" as the whole population was vegetarian. The vegetarianism is relevant to the plot, since not only were the children in this church not getting the inoculations of growth hormone the other kids were getting, they also weren't eating the beef and milk from the cattle who were also getting the hormones.
In "Clyde Bruckman's Final Repose", the titular character tells Scully she won't die. One wonders how that's possible, till we reach "Tithonus", where an immortal photographer apparently gives up his immortality in order to save Scully, taking her place. As this is how he stated he became immortal in the first place...
The doctor also notes that Scully is recovering from her gun shot wound at a faster rate than the doctor had ever seen...
I was rewatching the series and I found myself becoming slightly frustrated. Several times Mulder had the chance to shoot fleeing suspects and did not shoot (meanwhile Scully and Skinner don't hesitate to open fire in the same situations). At first this frustrated me and it seemed like the writers trying to extend the episodes. Then it hit me, early in the series Mulder shot one of the aliens which bled green acidic blood, this almost killed him. It makes perfect sense, Mulder is afraid to shoot because he might be dealing with an alien shapeshifter and shooting would make the situation worse, especially since unlike Scully or Skinner, Mulder has color vision problems and is probably afraid he won't see what color his target's blood is.
... Why would he shoot someone who's *running away*? If anything, we should be questioning why so many characters are so trigger-happy and shoot in circumstances other than self defence or defence of other people.
In the cold open to "Revelations", the unnamed preacher's stigmata looks like a Special Effects Failure uncharacteristic of the show... Then after the title sequence, we learn he was faking his stigmata with a bag of fake blood concealed inside his clothes - It looked like a bad special effect because it was a bad special effect in-universe. They probably had to walk a fine line with that scene - it had to look just real enough that the congregation would be believably fooled, but at the same time if it looked too real, it could induce fridge logic about just why this crooked preacher was so good at practical effects.
In the climax to "Unruhe", Gerry Schnauz kidnaps Scully and attempts to lobotomize her, thinking he's saving her from the "howlers" he sees around her. When Scully insists she's well, he points at a specific place they're supposedly emanating from... Which, later in the season, turns out to be the exact place Scully gets a brain tumor. If the Foreshadowing isn't purely symbolic, this could mean that the howlers did exist and were in fact a sign that his victims were unwell in some way; he was just drastically misinterpreting what they signified due to his Freudian Excuse.
In "Chinga", the title character has "The Hokey Pokey" as a leitmotif: This makes for deliberate Soundtrack Dissonance, but in a weird way the song's content does fit the plot: Chinga's main power is forcing people to do things against their will, and the lyrics to "The Hokey Pokey" consist of the singer telling the listener what to do.
By the time of "Field Trip", Mulder has been partners with Scully for six years, making him used to her skepticism. However, she accepts seeing the alien in his apartment as real so easily that he himself begins to doubt his own reality; ironically, him being the skeptic for once allows him to save them both from their Mushroom Samba.
"The Sixth Extinction II: Amor Fati" has the Cigarette-Smoking Man smoke two cigarettes at once when he is driving Mulder to his supposed home. When you take into account the fact that Mulder is inside a "Last Temptation-style dream", you'll realise that Mulder's personality is projecting onto the Cigarette-Smoking Man. Mulder would not trust that man so early in his dream, so it would make sense for him to flanderize him.
The changed title sequence for Season 8 includes Mulder falling into an eye; It sort of makes sense as a way of referring to his absence without departing from the surreal, symbolic feel of the rest of the opening, but I wasn't sure why it was an eye... Then I paid attention to the green color of the iris and realized it was specifically meant to be Scully's eye: Scully started to become more open to the paranormal during that season, so it's possible this symbolizes how having worked with Mulder has changed how she sees things.
Mulder's belief in the new mini-series that the events of 9/11 were a false flag event make sense when you consider that in his world it was tried once before.
Byers is always seen in a suit and tie, well-groomed and impeccably polite, but he has no need to be...right? After all, he got canned from the FCC, his worldview's been flushed down the toilet, Eagleland type two is in full effect, and he's living with a couple of fellows with much rougher manners and appearance. But that's exactly the point. It's going Crazy Sane. He maintains the appearance and manners of a gentleman and the demeanor of a Eagleland Type 1 in a world that laughs at it as an act of defiance. Just because the world's gone to hell in a handbasket doesn't mean he has to lower his own standards to match.
Mulder being a 9/11 Truther in season 10 was criticized by a wide range of people, but it may have been a gag that went over the heads of fans unfamiliar with the role the series plays in the Truther conspiracy. The pilot episode of the Lone Gunmen spin-off is notable for basically revolving around the motives for the 9/11 conspiracy as ascribed by the Truthers and airing several months before the actual attacks. The fact that Mulder believes in a conspiracy that uses the show as a major point in their argument is all kinds of meta-fun.
Season 11 contained the reveal of William's parentage: that the Cigarette Smoking Man was the real father due to him artificial inseminating Scully Many fans cried foul at this twist for coming out of nowhere, but it actually calls back to another episode: "Providence". In that episode, a UFO cult leader, Josepho, heard a prophecy from God that described William as "a future saviour coveted by forces of good and evil". It begs the question: if Scully is the good, then how could Mulder ever represent the bad, considering his search for the government's truth?
"My Struggle IV" ended with the CSM's death by being shot and falling into the ocean. It's neat because he has spent his whole life being a chainsmoker who survived an air strike, of all things. His body was mostly burnt, but he got through it in the end. So it's only fitting that his death concludes with the opposite of fire: water.
In "One Breathe," Maggie Scully tells Mulder a childhood story about Dana that exemplifies her compassion. The framing device, however, is her brothers taking her out in the woods to shoot BB guns, which explains why Scully has Improbable Aiming Skills despite being the scientist in this partnership and the one with less field experience.
The show's tagline ("The truth is out there") has a double meaning. On one hand, Mulder is seeking the truth about the alien conspiracy and the disappearance of his sister, but he doesn't know where to find this truth. Therefore, the truth is out there, as the answers he seeks are out in the world somewhere. On the other hand, the truth about the world is that many supernatural or otherworldly things exist and "normal" is just an illusion. Therefore, the truth is out there, as in what's real is actually very weird.
In "Bad Blood", a lot of time is spent describing Hartwell's teeth, with Mulder and Scully fighting about the look of them. Turns out, aside from a small overbite, they look totally normal. Also turns out, this is usual for vampires, and he is one, with Ronnie and his veneers being the odd one out.
The funeral home in "Bad Blood" is called PEACEFUL SLUMBERS FUNERAL HOME. Well, they sell their coffins to vampires to sleep in, so peaceful slumber is more of an advertisement for their comfy coffins than an euphemism for a dignified burial.
Mulders first name, Fox. When we first meet him, he is on a wild goose chase.
In 'Obliette', Mulder is heavily invested in the abduction case and was distraught when Lucy died. While it was never mentioned in the episode itself, it is clear that he relates to the victims because his sister was also an abduction victim who was never found.
In "The Calusari", we know Michael, who is essentially a ghost can travel around and physically harm people. He's a lot creepier and more emotionless than Charlie... which is exactly how the boy in the opening appears. Which means that kid might have been Michael, not Charlie, which then makes one wonder, how often has that happened? How many times have the parents walked around thinking they were with Charlie, and instead had the dead one?
In the first part of the Season Eight finale, Doggett calls his friend Agent Crane in on the weekend to help investigate a murder, which Crane mentions caused him to miss his "kid's Little League game." Then at the end of the episode we find out that Crane is one of the alien Replicants with the bumpy metallic spines. Assuming that he does have a family, they're living with a murderous alien and are absolutely none the wiser...
Or, even worse, he was replaced before he met his wife and had a family. That means his child is a Half-Human Hybrid and just hasn't realised it yet.
"The Jersey Devil"'s ending; both of that... creature’s parents are dead. That means she's either going to starve to death or a pack of passing coyotes will decide "ooh, easy lunch" and eat the poor child alive. Poor kid.
And, to say that the female Jersey Devil deserved to die is just cruel. She was trying to escape, and was not actively attacking Mulder, Scully or anyone else. Despite her, ahem, dietary preferences, Mulder's shock at the fact the resident Corrupt Cop killed her is entirely justified. And makes us hate the Corrupt Cop more.
