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.
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.
"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.
Quite a bit, but the most notorious example might be from Fight the Future: how did Mulder and Scully get back to civilization from the crashed spaceship in the Antarctic? (There's a joke about this later in the TV series.)
Okay, "Home" is a great and chilling episode, but does anyone else think the writers didn't put much thought into that ending? The surviving Peacock family hit the road with plans to start over their grotesque family elsewhere, but how in blazes do they hope to pull that off? The only way they had managed to hide from society for so long was because of their ancestral farmhouse, which they no longer have by the end, and in the course of the episode they had murdered two law-enforcement officers and one's innocent wife, so there's no doubt whatsoever that police will be actively looking for them. Since they aren't supernatural villains with any reality-bending powers, it's a pretty safe bet that the minute their car runs low on gas or they need to find food, Peacock Jr. and his incestuous potato-sack of a momma are fucked.
They're also going to have some problems raising another family. Sure, Momma just had another baby, but it most likely would have died naturally anyway, and she's getting pretty old to be having more....
On the other hand, it's fair to say that these people aren't exactly completely rational or psychologically healthy, and the whole point of the episode is that they've become locked in a very unhealthy and awful cycle. They're starting again and doing the exact same thing because, horrible it may be, it's the only way of life they know, not because it's a foolproof idea that's guaranteed to work out. We only see that they're trying again, there's nothing to suggest that they absolutely definitely succeed.
The "police are actively searching for them" forest seems a tad more pertinent than the few "can they still make babies" trees. The ending presents them as Karma Houdinis free to continue their horrific lifestyle, but they absolutely don't have the smarts or resources to outwit authorities that are definitely pissed off and hunting them down.
Easy Logistics played for the Rule of Cool: Mulder never ever has any qualms about commandeering any resource from the FBI, regardless the cost, which strikes as unrealistic when everyone knows he is acting on suspicions, insignificant clues and in most cases outside the rule of law, full stop. Airplane (possibly military) transport, all-terrain tracked vehicle, supplies by ton for the Antarctic trip. No higher FBI official batted an eyelash on such extravagances ever.
The girl handling the agents' finances was later revealed to be a huge fan of the agents, so she probably didn't treat any of Mulder's actions as unnecessary.
Mulder is also implied to have come from a wealthy family; he grew up on Martha's Vineyard, his parents owned a summer house in Connecticut, he went to Oxford for college, and he "rents" a Congressman for his own uses. In season 8, he's unconcerned about his own unemployment and doesn't try to get another job. After that, he's able to easily slip into hiding and support himself while doing so. It could be that he's not using FBI channels or money at all, but his own money to fund some of his more ambitious expeditions and his friends in high places (see the rented Congressman) to grease the wheels.
"Darkness Falls" episode (1994) does it at least twice. The Monsters of the Week, basically vicious blood-sucking bugs, are "afraid" of light in Mulder's words, in practice they are inactivated by light. Our heroes and a few others are caught at night in stranded cars, but with fully operational engines and electrical systems. Why didn't they turn on the headlights and interior dome lights? And how could the bugs after killing a 70-90 kg (155-200 lbs) man raise his body onto a tree? (Although the last one can be explained by the fact the victim could have been killed while he was already up in the tree, since he was a logger).
There was supposed to be critically short fuel supplies, making escape (or even cabin lighting) via the vehicles impossible. What struck me as odd is why they didn't maintain a small to medium reserve to use as an extreme form of lighter-fluid, and use it to start campfires that, once going, would have the unlimited fuel of the forest.
Speaking as someone who's grown up in The Other Rainforest, at that location and time of year, any wood they didn't have chopped and stacked under cover was probably too damp to burn. Even lighter fluid sometimes isn't enough to keep a fire going, if it's too soggy.
Scully giving William up for adoption in season 9 is a source of Fridge Logic for a lot of fans. In the first place, it goes directly against Scully's character, who only four seasons before had fought tooth-and-nail to adopt a three-year-old daughter she'd never met and had only known three days. All this despite knowing that the child was conceived to be experimented on and that both mother and daughter would likely be hunted by the conspiracy. In the second place, it doesn't make sense from a common sense standpoint. Scully gives William away to an anonymous couple in order to keep him safe. Never mind that she is taking the baby away from at least five trained FBI agents who know the details of the situation and have the weapons, knowledge, and training to at least try to keep him safe and giving him to a couple who know nothing about the baby's paranormal background, the conspiracy, or the fact that they now have a huge bulls-eye painted on their backs. To make it worse, this is a closed adoption—there is nothing Scully can do to check on her baby after she gives him up. Doesn't this just make it easier for the conspiracy to kill of William and his adoptive parents?
With The revival is heavily implied that this was Chris plan all along. William was conceived right after Mulder discovered the truth about Samantha taking away any personal stake he had on the X-files. So losing him give him and Scully a new crusade besides fighting the invasion. Specially if you take in account that Cancer Man "dies" in the same episode Scully announces her pregnancy and reappears right after she gaves him up for adoption showing he has been manipulating Mulder behind scenes for God only knows how long. In fact he might had sent the note that made Mulder get away so a vulnerable Scully could be convinced that adoption was the only way to keep their baby safe now that Mulder was M.I.A. Did Spender ever explained how he got away from his torturers? Those tears might not had been about being happy to met his nephew but about tricking Scully to save his neck.
The season five episode "Folie à Deux" has a nice little whammy. A guy in an office building can see a bug monster disguised as his boss (which no one else can see) turning his co-workers into zombies (which no one else can see either). He sends a tape to a radio station containing a warning telling everyone to band together and hunt down the monster that 'hides in the light.' Eventually, he gets desperate enough that he pulls out an assault rifle and takes everyone hostage, separating out the 'zombies' from the real people and even getting his bug boss singled out on the floor right in front of him. He then... threatens to start shooting real people unless he gets on TV. He has both the bug and the zombies RIGHT THERE, why doesn't he just shoot them now?
Because he wanted to prove that he wasn't mad rather than being remembered as the psycho who killed his colleagues for no apparent reason. Sure, one might argue that the true nature of Pincus would be revealed once he died. On the other hand, he is able to trick cameras into depicting him as human, so who knows whether these effects would not persist after death?
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... child's (I refuse to use the word "creature") 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 (like some critics who reviewed the episode) 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.