At the end of the first movie, Scully talks about the vaccine that saved her, saying that it could cure people from the alien virus. It could also seriously mess up with the upcoming alien invasion. Sigh, the agents decided to pursue other things.
During Season 6-7 the Syndicate was destroyed at the hands of the Alien Rebels. At the time, the writers spoke of their plans for a new Syndicate, headed by Alex Krycek and Marita Covarrubias. This plotline was set up in "Requiem" but never resurfaced.
Adventure Towns: The Dynamic Duo chases aliens, alien-human hybrids, clones, genetic mutants, vampires, serial killers or conspirators and encounters weird phenomena all over the United States. Plus in Norway, Hong Kong, Russia and Antarctica.
Affectionate Gesture to the Head: Mulder and Scully would touch each other's forehead, stroke each other's hair, hold each other's head or cup each other's face. UST at its best.
Alien Abduction: A common theme, although it's usually ambiguous whether extraterrestrials or human conspirators are actually responsible for it. Both Scully and Mulder were victims of it, among many others.
Mulder acquires videotape of one such autopsy in "Nisei". Scully suspects it of being a fake, only it turns out that there's some truth to it.
Mulder personally observes one in "Gethsemane". However, an informant who worked for the Department of Defense claims that the subject of the autopsy was not a real alien but only what "they" wanted Mulder to see.
Always Save the Girl: In the very first episode, Mulder said that nothing else mattered to him except finding out the truth about the conspiracy and what happened to his sister. Early seasons of the show got a lot of mileage out of making him choose between pursuing his quest and saving Scully. Around the beginning of season 5, though, it pretty much ceased to even be an issue — he decided Scully was priority #1 and never looked back. (She saves his butt just as often, of course.)
Scully remains a hardcore skeptic long after she's seen shape-shifting aliens, watched Mulder be mind-controlled into things he'd never do on his own, etc. It's somewhat justified, though: later seasons tended to imply that Scully felt she had to take a more skeptical stance than she really believed anymore in order to keep Mulder's wacky ideas grounded.
Even Mulder refused to believe in anything that was close to miracles and religiously paranormal stuff. In episode "3", he doesn't believe in vampires, that were real.
Arc Words: "Trust no one", Deep Throat's last words which come up various times throughout the series.
Ascended Extra: The Cigarette-Smoking Man had four brief, mostly wordless appearances in the first season, doing little beyond hover in the background smoking. His role gradually expanded, and by the middle of Season Two he was firmly established as the show's Big Bad.
Badass Longcoat: Nearly omnipresent trope for most of the characters. The FBI wear them, the conspirators wear them, the mysterious informants wear them, everybody wears them! They all wear long trench coats or lab coats, and they all look awesome in them.
Bad Black Barf: An alien virus called "Black Oil" caused black liquid to come out of the mouth, nose and eyes of its victims.
The Bad Guy Wins: Well, the good guys don't, anyway. Sure, at the end of the finale CSM and Rohrer are both dead and Mulder has escaped. However, many of the conspirators are still alive, our heroes have been forced into a life on the run, they have just discovered the date of a planned alien invasion and are no closer to stopping the alien takeover than they were at the beginning of the pilot.
Bag of Holding: Mulder's and Scully's pockets. Boy, do they have to be deep and spacious! They have there their FBI badges, mobile phones, wallet/purse, calling cards, coins, keys, pens, latex gloves, bags for collecting evidence, flash-lights of various sizes, and Mulder occasionally pulls sunflower seeds out of there.
Bat Signal: Mulder summons his informants by switching on blue light lamp in his apartment (Deep Throat) and by putting the iconic X sign from masking tape on the window pane (Mr. X).
Beautiful Dreamer: Used fairly frequently as a device for UST and to show how close and dedicated to each other Mulder and Scully are. When either of them was in the hospital, the other kept a vigil at the bedside. The following quote illustrating the trope is from "Redux II":
Mulder: I came by last night, but I... I didn't have the heart to wake you.
Berserk Button: Do not come between Mulder and Scully. No, really. It's a bad idea. That goes for both of them, by the way.
The Big Board: The X-Files office has bulletin boards and walls covered with pictures, photos and newspaper clippings concerning the paranormal and the cases Mulder and Scully were working on. In addition, they often used slide shows to present cases. Considering Mulder's interest in the paranormal and the level of his obsession, some might consider his office to be a Room Full of Crazy.
Bittersweet Ending: At the end of the show, the Government Conspiracy has taken some hits but is still going strong, and alien colonization of Earth is supposedly inevitable and proceeding on schedule for 2012. Mulder and Scully are on the run from a death sentence... but they're both alive, and they're together, and that means maybe there's hope.
Harlan Ellison was complaining about this as early as the first season, apparently, leading to a scene where the Cigarette-Smoking Man explains that killing Mulder would "turn one man's religion into a crusade." (Which still comes across as sort of a Hand Wave, as they've killed plenty of dogged investigators before Mulder and The Conspiracy has remained intact.)
"Requiem," which was written without knowing whether it would be the final episode, has a number of callbacks to the pilot episode. Mulder and Scully go back to Bellefleur, Oregon, which was the location of their very first assignment. They see a faded X sign on the road, which Mulder painted there to mark an anomalous electrical disturbance back then. They also meet some of the same people, some of which are multiple alien abductees. In both episodes, Mulder and Scully have a personal conversation in a hotel room — in the pilot Mulder tells her "nothing else matters to [him]" except his quest, while in "Requiem," he insists that the quest isn't worth sacrificing her health and happiness.
The series' actual finale, "The Truth," contains yet another hotel room chat, in which Mulder and Scully explicitly reminisce about the first one.
Breather Episode: The comic relief episodes actually provided some of the more interesting and innovative filler and served to counterbalance some of the more ridiculous serious episodes as the series went on.
Captain's Log: Early seasons had Scully (and sometimes Mulder) writing case reports at the end of many of the Monster of the Week episodes. In the final seasons, after David Duchovny left the show, Scully read her journal entries as letters to the missing Mulder.
Chilly Reception: Mulder toward Scully initially; later, either of them towards anyone replacing the other (especially between Scully and Fowley).
Cloning Blues: First done in an early Monster of the Week episode with Myth Arc elements "Eve" and the trope keeps resurfacing in the mythology, e.g. "End Game", "Colony", "Herrenvolk" or "Memento Mori".
Deadly Doctor: Evil doctors collaborate with the conspiracy, having no scruples performing experiments on people.
Deadly Nosebleed: She doesn't actually die of it, but this is the only visible symptom when Scully has terminal cancer.
Deal with the Devil: Skinner makes one with the Smoking Man to save Scully's life in season four. Mulder came close to doing the same, but ultimately didn't because he wouldn't have been able to face her afterward.
Deus Angst Machina: The main characters get a disproportionate number of metaphorical Groin Kicks just within the few years in which the show takes place. Mulder has both parents die and is constantly tormented by people who appear to be his sister but aren't, but Scully takes the cake having one parent and her sister die (the sister being at least partly her fault) and the entire abduction plotline.
Exposition Of Immortality: Mulder and Scully run across a couple of long-lived characters during the series' lifetime; the first example is in "Squeeze," when Mulder is shown photos of Eugene Tooms that demonstrate he hasn't aged since 1933.
Eyeless Face: The alien rebels have their eyes, ears and mouth sealed up so they can't be infested with the 'black oil'.
Eye Scream: The alien rebels sewn up eyes definitely count. Creepy as hell!
First Name Basis: Agent Doggett and Agent Reyes always call each other John and Monica, unless other agents are around. This likely comes from their time spent working together on the kidnapping and murder of Doggett's son years prior.
Friend or Idol Decision: Mulder has to choose between saving Scully and finding Samantha and/or the truth about the Government Conspiracy several times over the course of the show — most explicitly in "Endgame," but it also comes up more subtly in "Demons," "Redux," "Redux II," "The Sixth Extinction: Amor Fati" and "Requiem."
Mulder: Looks like the fuselage of a plane. Scully: It's a North-American P-51 Mustang. Mulder: I just got very turned on.
Or the one from "Chinga":
Mulder: Maybe you don't know what you're looking for. Scully: Like evidence of conjury or the black arts, or shamanism, divination, wicca or any kind of pagan or neopagan practices. Charms, cards, familiars, bloodstones, or hex signs or any kind of ritual tableaux associated with the occult, santeria, voudoun, macumba, or any high or low magic. Mulder: Scully? Scully: Yes? Mulder: Marry me.
This one from "War of the Coprophages":
Scully: The very idea of intelligent alien life is not only astronomically improbable but, at its most basic level, downright anti-Darwinian. Mulder: Scully... what are you wearing?
Hide Your Pregnancy: Season 2 started to shoot as Anderson was pregnant. First was this (Scully is shot mostly seated, wearing jumpsuits, or in "unflattering angles"), then Scully got abducted just to avoid it. (see Written-In Absence.)
Hollywood Healing: Mulder, Scully and Skinner get shot and beaten up very badly many times but don't worry, neither of them has any nasty permanent scars whatsoever.
The really horrible example is "Fight Club". Mulder's and Scully's faces are badly battered, bruised; they have stitches and Mulder's jaw is even wired, and his arm is broken. They are a sorry sight indeed, and they've beaten up one another! Because of some half-sister doppelgängerish encounter. By the next episode, they're fine.
Averted in "The Pine Bluff Variant" when Mulder gets tortured and in the next episode "Folie a Deux", his fingers are still bandaged.
Also averted in "731": At the end of the episode Mulder's face bears very visible and believable marks from a severe beating.
Hot Scientist: Scully herself, Dr. Bambi Berenbaum the entomologist from "War of the Coprophages", Lisa Ianelli the cryobiologist from "Synchrony" and Susanne Modeski the troubled organic chemist from "Unusual Suspects" and "Three of a Kind".
Huge Guy, Tiny Girl: The show came up with the Scully Box because David Duchovny is almost a foot taller than Gillian Anderson. In the few scenes that were shot without the box (or Scully in very high heels), Anderson barely reaches Duchovny's shoulder.
Idiosyncratic Episode Naming: The Myth Arc episodes (often two-parters or trilogies) sometimes used complementary names as "The End"/"The Beginning", "Two Fathers"/"One Son", "Biogenesis"/"The Sixth Extinction I & II" or "Within"/"Without". The standalone episodes' titles were often extremely vague words or phrases brought up by a single line of dialogue or some other subtle or insignificant aspect of the episode, sometimes in a foreign language. The show famously played a game with its fans who tried to find meaning in anything, no matter how obscure or insignificant it might appear, including the names of the episodes.
If Jesus Then Aliens: Averted. Scully is Catholic and believes in miracles, but is a hardcore skeptic about all other paranormal phenomena; Mulder is agnostic and rather cynical about organized religion but believes in basically everything else. (It's implied at least once that God is deliberately hiding himself from Mulder's perception as a test of Scully's faith.)
Mulder and Scully to each other other. Mulder says he even made his parents call him Mulder, but it doesn't seem to have stuck. Mulder occasionally called Scully "Dana" at emotional moments in the first few seasons, then mostly gave it up, as if the last names had actually become more intimate by that point. Scully never even tried to call him Fox after the first time.
Living Emotional Crutch: Both Mulder and Scully become this to each other, verging on Heroic BSOD whenever they're involuntarily separated. This is portrayed as basically a good thing; their relationship ends up helping both of them overcome their personal issues to some degree.
Longing Look: Mulder and Scully had an astonishing talent for giving each other looks so singular, emotional and full of meaning they made anyone else in the room — or on the other side of the television screen — feel like they were intruding on some absurdly private moment.
Long Runner Cast Turnover: By the time the series ended, only AD Skinner remained a main character. Mulder, Scully, and the Cigarette-Smoking Man were all demoted to regulars or extras.
Loved I Not Honor More: Subverted. Several times the show puts Mulder in what looks like a Friend or Idol Decision between saving Scully and his quest for the Truth — but ultimately it's strongly implied that the only reason he's able to achieve any success in his quest is because he has Scully as his partner.
My Biological Clock Is Ticking: Scully's abduction left her infertile. It's a source of angst for her. It's played much more subtly — and with good reason; he'd never be enough of a jerkass to actually bring it up, considering Scully's infertility — but Mulder is implied to be somewhat wistful about not being in a position to have kids too.
No Hugging, No Kissing: The show was famous for this early on, but even then it was oddly subverted in a few instances, and by around season 6 Mulder and Scully had really become awfully, uh, cuddly for platonic friends.
No Sense of Personal Space: Mulder in regards to Scully, as well as being quite affectionate. She is definitely unnerved by it in the early seasons, but eventually gets used to it.
Not Love Interest: While it took them seven seasons to get around to making it official, for all intents and purposes Mulder and Scully were best friends/lovers/spouses since day one. It could even be argued that their bond transcended all three of those roles to become something more all-encompassing than most people ever experience. It certainly cannot be denied that they were the most important people in each others' lives almost since the first time Scully walked into Mulder's basement office.
Not of This Earth: The mysterious bacteria and virus, first appearing in "The Erlenmeyer Flask".
Dr. Carpenter: A fifth and sixth DNA nucleotide. A new base pair. Agent Scully, what are you looking at... it exists nowhere in nature. It would have to be, by definition... extraterrestrial.
Quite a few monsters of the week are shown to have survived their presumed deaths, from the flukeman in "The Host" to the rogue A.I. in "Ghost in the Machine", but very few of them ever show up again — which makes one wonder where exactly they went.
Mulder on more than one occasion.
Krycek, many times.
The Cigarette-Smoking Man in season 5 and again in season 7.
Jeffrey Spender, presumed dead in season six, but seen again in season nine.
Obstructive Bureaucrat: Practically everyone else in the FBI except for Skinner. In particular, Kersh and Follmer.
One Steve Limit: Averted — there are at least four fairly important characters named William, three of whom go by the nickname Bill: Mulder's father, Scully's father, Scully's older brother, and Baby William. And it's Mulder's middle name.
The Pete Best: Not the same character exactly, but the principle applies: Charles Cioffi as SCI Blevins, Mulder and Scully's boss in the Pilot and Conduit, was intended as a regular character but Cioffi proved unable to continue in the role (though he did reappear in the Gethsemane/Redux arc in Seasons 4-5). He was replaced in Fallen Angel by the one-off character Section Chief McGrath, played by Frederick Coffin. Finally, Mitch Pileggi played Skinner in Tooms and the rest is history.
Police Are Useless: Zigzagged. Mulder and Scully are themselves police and extremely competent, hence an aversion. Other cops, be they local police or other FBI agents, can be all over the place: genuinely helpful, well-meaning but ineffectual, obstructive bureaucrats or in cahoots with the Syndicate/Monster of the Week.
Politically Incorrect Villain: The Consortium as a whole. The upper levels seem to be composed entirely of older, upper-class white men. They also consistently failed to realize it was Mulder and Scully as partners, not Mulder individually, who might pose a threat to their plans, thinking of Scully only as Mulder's Berserk Button when they could be bothered to notice her existence at all.
Porn Stash: It's a recurring joke that Mulder has one. Unusually for the trope, he makes no real attempt to keep it secret, and Scully doesn't seem to care beyond thinking it's kind of silly.
Mulder: Whatever tape you found in that VCR? It isn't mine. Scully: Don't worry, I put it in the drawer with all the other videos that aren't yours.
Power of Trust: "Trust no one" is a major catch phrase in the show, but it's subtly ironic — one of the show's main themes is actually the importance, in a world of lies and conspiracies, of having someone you can trust absolutely. Mulder and Scully spend so much time saying things like "You're the only one I trust," it became a common fandom joke that they were just using "trust" as a code word for "love."
Agent Spender, who's killed by his own father, the Cigarette-Smoking Man, after handing the X-Files back to Mulder. Except that the last season episode "William" reveals that he didn't die. Instead, he was subjected to experiments that left him horribly disfigured.
And the Well-Manicured Man.
Red Herring: Red Herrings were used on the Myth Arc level as well in some standalone episodes. Several clues that appeared to be important to the mysteries the agents Mulder and Scully were supposed to unravel ultimately lead nowhere, or were not simply addressed again.
The fate of Samantha Mulder was probably the biggest Red Herring of the series. Her abduction was a defining moment of Mulder's life as it triggered his belief in the paranormal and motivated his career at the FBI. Throughout the series, Mulder was tormented by her clones and reassurances that she's still alive. However, it was revealed that she had been abducted by the conspiracy who had collaborated with the aliens. She was saved by some strange kind of fairies or angels which made her body disappear, meaning that her corpse will never be found, but Mulder did see her ghost.
"Red Museum" is basically one big Red Herring. Viewers are teased by teenagers' weird kidnappings, the cult, a doctor's plane crash, cattle inoculation, or a peeping tom, but none bear significance for the resolution of the case. The episode appears to be a Monster of the Week story, but it turns out to be connected to the Myth Arc. However, those plots or characters did not resurface in the later mythology episodes.
Relationship Upgrade: Scully and Mulder, but it happened offscreen and it's not clear exactly when. The leading candidate is in season 7's "all things," which features Scully evaluating her past choices about life and relationships, leading up to a scene where she's getting dressed in Mulder's bathroom while he's asleep in bed, apparently naked.
Rewind, Replay, Repeat: Happens frequently, usually when Mulder catches a glimpse of something in the footage that everyone else overlooked.
A lot for Scully and Mulder, although they were mostly relatively restrained about it until around season 6.
The writers were also very aware of other shippers in the fandom, including the slash fans, and enjoyed throwing out occasional bones for the Scully×Skinner, Mulder×Skinner, and Mulder×Krycek crowds.
Single Issue Psychology: A lot of Mulder's issues go back to his younger sister's abduction while they were home alone together when he was 12. He actually calls Scully out for assuming everything he does is about his sister in "Oubliette," although in that episode she's entirely correct.
Soundtrack Dissonance: A favorite technique when coupled with the Gory Discretion Shot: something horrible would start to happen, and the camera would pan away, with cheerful incidental music being underscored by the sound of whatever godawful thing was happening. Used memorably in "Never Again" and "Home."
Start to Corpse: Varies, but episodes frequently opened with unfortunate victims dying in mysterious ways, so it was often pretty close to zero.
Stating the Simple Solution: The First Elder constantly suggests killing Mulder... only to be overruled by the other conspiracy members, who are either feeding him information or manipulating him for their own purposes.
X was very different from Deep Throat, replacing grandfatherly benevolence with deadly pragmatism.
Marita, X's replacement, was quite different from either of her predecessors and turned out to be a mole to boot.
Doggett and Reyes were very different from Mulder and Scully, replacing the Absolute Believer/Healthy Skeptic dichotomy with Absolute Skeptic/Open-Minded, and replacing Mulder and Scully's Masculine Girl, Feminine Boy with a more conventional gender dynamic. While they become close, they're never as emotionally dependent on each other as Mulder and Scully could be even before they were romantically involved, and they're on a First Name Basis right from the start.
Sympathetic Murderer: Very common. You're usually supposed to feel at least some degree of sympathy for the monster, even if Mulder and Scully end up having to kill it.
There Are No Therapists: Interestingly averted in the earlier seasons, at least for Scully. She sees a therapist a few times after her abduction in season two.
To Be Continued: They had several two-parters and trilogies. Some mythology stories ended with this as well, and the next episode would be a standalone one.
Voluntary Shapeshifting: Various baddies, but the most prominent example is the Alien Bounty Hunter, a recurring antagonist. He's an extraterrestrial assassin, and can look like anyone.
Was It Really Worth It?: Various characters towards Mulder's quest, and Scully's involvement gets questioned as well. One of the most prominent cases is Bill Scully in "Redux II", accusing Mulder that it's his fault that he has lost one sister and is losing another, belittling Mulder and Scully's fight to reveal the truth and uncover the conspiracy as search for "little green men".
Why Don't You Just Shoot Him?: Even disregarding the rather questionable justification for the bad guys not simply offing Mulder as they've done with so many other people (that Mulder would become a martyr), they don't even seem to try to discredit him that much.
"The X-Files" sound way better than "the U-Files". They might have been called that for "unsolved" but weren't thanks to the filing system at the FBI in the 50's.
Clerk Bahnsen: It's in an X-file. Agent Dales: An "X-file"? Clerk Bahnsen: Yes, unsolved cases. I file them under "X". Agent Dales: Why don't you file them under "U" for "unsolved"? Clerk Bahnsen: That's what I did until I ran out of room. Plenty of room in the "X"s.
Accentuate the Negative: In "One Breath", when Melissa Scully calls Mulder out for doing this while trying to convince him to go to the hospital to see Dana, who is dying:
Melissa Scully: I don't have to be psychic to see that you're in a very dark place. Much darker than where my sister is. Willingly walking deeper into darkness cannot help her at all. Only the light... Mulder:(disgustedly) Oh, enough! — with the harmonic convergence crap, okay, you're not saying anything to me. Melissa Scully:(angrily) Why don't you just drop your cynicism and your paranoia and your defeat. You know, just because it's positive and good, doesn't mean it's silly or trite. Why is it so much easier for you to run around trying to get even than just expressing to her how you feel? I expect more from you. Dana expects more. Even if it doesn’t bring her back, at least she’ll know. And so will you.
Alice Allusion: In "Paper Hearts", Agent Mulder has to face again John Lee Roche, a convicted Serial Killer of little girls who was caught thanks to Mulder's psychological profile. He cut cloth hearts from his victims' clothes and kept them hidden in a copy of Alice in Wonderland. The phrase 'Mad Hat' appeared in Mulder's dreams and it was also a mark at a newly found crime scene. Roche used to live in Alice Road in Boston, and Mulder concludes that that's how he got the idea and that he took the role of the Hatter.
Almighty Janitor: One episode only, but then he can take on different faces, which makes him pretty powerful as far as Janitors go.
Anal Probing: Referenced and Played With often. In "Jose Chung's From Outer Space", for instance, it's Scully's opinion that a young couple whom Mulder believes were abducted by aliens were only engaging in sexual activity before they're old enough to handle it. Mulder, not seeing how this could discredit the girl's interpretation of events as revealed under hypnosis (which resembles the typical Alien Abduction story), asks his partner, "So what if they had sex?" to which Scully responds, "So we know it wasn't an alien that probed her."
Apocalypse Anarchy: In "War of Coprophages". People think that they are all going to be killed by cockroaches which got there either due to government conspiracy and their experiments, or that they are alien robotic invaders. Chaos ensues. It's most apparent in one scene in a convenience store where everybody is trying to grab whatever supplies they can and two ladies fight over the last can of insecticide.
In "Teso Dos Bichos", a hoard of sewer killer pussy cats were filling an Absurdly Spacious Sewer with dead bodies but the cats were not seen triumphantly sitting atop of them.
In "Detour", Mulder and Scully fell into a pit full of dead and injured people that were dragged there by the monsters of the week. They tried to stack them so that they could get out of the pit.
Audio Erotica: Chantal misses Mulder's sexy voice in "Small Potatoes". Considering that she's a phone sex operator, one must take it with a pinch of salt.
Author Avatar: In-universe example: the protagonist of the Cigarette-Smoking Man's rejected manuscripts, Jack Colquitt.
Autopsy Snack Time: Scully in "Bad Blood" examines the stomach contents and finds half-digested pizza appetising. Later she orders a pizza for dinner.
Away In A Manger: Baby William's birth is this trope, though he's born in late May rather than December. This includes the proverbial Star Of Bethlehem (which leads Mulder to the abandoned town where Scully gave birth) and the Three Wise Men as portrayed by the Lone Gunmen. An interesting birth, given that Mulder is a agnostic and Scully a Catholic—the symbolism probably wasn't missed by either of them.
Darren Peter Oswald in "D.P.O." It's safe to say that if you associate with him at all, you're putting yourself in serious peril.
Cecil L'Ively, Ellen Adderly, and the transformed Ray Pearce also qualify.
Back to Front: "Redrum" made use of this, but the central character was aware of it. He woke up in prison, not understanding how he got there. He goes to sleep that night, and wakes up the next morning to discover that he is going to trial, for the crime he was incarcerated for "yesterday."
Before My Time: In "Travelers", Mulder goes to interview a retired FBI agent who investigated X-Files in The Fifties. The agent asks Mulder whether he's heard of the House Un-American Activities Committee, but immediately assumes that he hasn't. Even if he knew nothing about Mulder personally, the topic is covered in high school history classes.
The episode "Triangle" sees Mulder investigate a luxury passenger liner that mysteriously appears on the edge of the Bermuda Triangle. Once on board the ship, Mulder finds himself in the year 1939 as Nazi soldiers are fighting the British crew for control of the ship.
In a later episode, Area 51Man in Black Morris Fletcher claimed to be the one who originally coined the term and insisted that powerful, primal, other-worldly forces are hidden beneath the waves, waiting to be plucked by man.
Better Than Sex: In the episode "Jose Chung's From Outer Space", when a Lt. Jack Schaefer is speaking to Agent Mulder, he says, "Have you ever flown a flying saucer? Afterwards, sex seems trite."
Bait-and-Switch Gunshot: In "Pine Bluff Variant", Mulder is about to be shot but one of the terrorists is shot instead.
The Big Board: The FBI are using a big chalk blackboard for a hostage negotiation in "Duane Barry".
Blast Out: The opening to "Kill Switch". A rogue A.I. sends messages to several Washington D.C. drug dealers telling them that their arch rivals are meeting at this diner. All of them come and set up to wait. The final message is sent to a pair of U.S. Marshals, claiming that a fugitive is there, so they burst in to arrest him and cause a shootout. All to kill one nerdy guy in the middle booth.
Brown Note: In "Drive", a secret Navy communication device generates radio waves that vibrate at the same frequency as the human skull, inducing increasing intracranial pressure that literally blows the listener's brains out their ears unless the pressure is relieved surgically.
Burial at Sea: Scully's father, a Navy captain, is cremated and buried this way in "Beyond the Sea".
Casual Danger Dialog: Mulder has a tendency to do this. "The Pine Bluff Variant" has one of the better examples, when Mulder is undercover trying to infiltrate a domestic terrorist group. He's blindfolded, led into a warehouse, and has his hands strapped to a table.
Mulder: Is this the Pepsi Challenge? How ’bout some, uh, fresh air, boys? Terrorist: Welcome, Agent Mulder... This is just a little method that we use to learn the truth. Mulder: Well, you might want to put that hood back on me unless you want to see a grown man cry.
Cliffhanger Copout: Near the end of "Gethsemane", the fourth season finale, the audience sees Mulder alone in his apartment, crying with his gun in his hands. We cut away just before hearing his gun go off. The next scene is a flash forward in which Scully has apparently been called to his apartment to identify the body of a white male who died of a self-inflicted gunshot wound. She identifies it as Mulder. The next season begins by revealing that Scully was lying, the body is not Mulder's, and the whole crying holding his gun thing was not related to anything. (Specifically, Mulder probably was contemplating suicide — until he was distracted by evidence that he was being spied on, confronted the spy, ended up shooting him, and concocted a plan with Scully to fake his own death.)
Close Enough Timeline: "Dreamland". Everything gets set back to normal and the whole universe goes back to the way it was before the time rip — but Mulder's apartment is still cleaned up and has a waterbed, and Scully still has a dime and penny that were fused together by the warp in space-time, even though the events that caused both scenarios never happened. It could be explained that they weren't in the path of the snap-back. But how would time snap back for the whole universe then?
A fan theory holds that the time loop in "Monday" later in the same season was triggered by the universe repairing itself and trying to get rid of Mulder's waterbed, the last remaining evidence of the paradox. This makes a surprising amount of sense when you watch the episode — the starting point for each loop is the waterbed springing a leak.
Combat Stilettos: Scully wears them most of the time, sometimes even when she has no reason to be in work clothes and knew to expect trouble ahead of time.
Lampshaded in the episode "Hollywood A.D.", when an actress portraying Scully in a movie asks her how it's possible to run in heels that high.
In "2Shy", she used them as a self-defense weapon by kicking a serial killer in the face.
Ditto in "Leonard Betts".
Comforting Comforter: At the end of "all things", Scully falls asleep on the couch while talking to Mulder. He pauses to brush a lock of hair from her face and gaze at her before covering her with a blanket to be warm. A romantic example of the trope, since it's heavily implied they slept together for the first time later that night.
A rather nice one in "Soft Light": A man has inexplicably disappeared from his hotel room. Mulder, Scully, and a young detective search the room for evidence of what might have happened. Having witnessed the events of "Squeeze" and "Tooms", Mulder and Scully naturally check out the heating vent. Cue the detective saying "You don't think anyone could squeeze through there, do you?" and Mulder quipping "You never know".
There's a sweet Friendship Moment in "The Field Where I Died" (an episode coincidentally about past lives).
Scully: I wouldn't change a day. Well, except for that Flukeman thing. I could have lived without that just fine.
Converse with the Unconscious: In "One Breath," when Scully is returned after her abduction, Mulder is finally persuaded to go to her bedside and makes a sweet, awkward speech:
Mulder: I feel, Scully...that you believe...you're not ready to go. And you've always had the strength of your beliefs. I don't know if my being here will help...bring you back. But I'm here.
Coordinated Clothes: In the second half of the episode "Eve", the murderous girls wear matching red hellish outfits. It was probably a case of I Just Knew or Eve 7 might have bought the outfits for them. Their identical looks make them even more disturbing.
"Squeeze": Eugene Victor Tooms took small personal things from his victims, e.g. a coffee mug, an ornamental snowstorm or a hairbrush. Mulder and Scully found this kitschy collection of trophies in his apartment.
"Our Town": The town of cannibals kept their victims heads in a cabinet. They were found at Mr Chaco's, but the whole town was guilty.
"Paper Hearts": John Lee Roche was a serial killer who murdered sixteen little girls. He cut a piece of fabric in the shape of a heart from their clothes. He placed the cloth hearts in a copy of Alice in Wonderland and kept the book in his car, thus being the 'carrying the trophies by himself' variety.
Criminal Mind Games: Mulder was the target in "Young at Heart", quite possibly "Grotesque", then "Pusher" and "Kitsunegari".
"Unusual Suspects" does feature Mulder, but it's about and stars the Lone Gunmen. "Three of a Kind" is similarly about the Gunmen but has Scully around as a supporting character.
"Avatar", "Zero Sum" and "S.R. 819" focus on Skinner.
Deadly Bath: Both subverted ("Chinga" — the music builds, we're sure something creepy's going to happen, the phone rings and... it's Mulder, he's bored) and played straight ("Squeeze", "Irresistible").
Dead Man's Hand: "Clyde Bruckman's Final Repose" has the title character playing poker with Agent Scully and holding a full house of aces and eights with the ace of hearts as the fifth card. As one might suspect from the episode name, he dies.
In the Myth Arc episdode "Erlenmayer Flask", one unfortunate man or hybrid was thrown out of a window and they tried to make it look like a suicide.
It was also done in Monster of the Week episodes "Born Again" (defenestrated dirty cop) and in "Schizogeny" (a guy was pulled out of a room by trees).
Disposable Vagrant: Scully is informed in "731" about experiments performed on lepers, homeless and insane people. Quite interesting, actually, as they usually have no scruples about abducting anybody, not excluding their own family members or FBI agents.
Dresses the Same: Played with in "How the Ghosts Stole Christmas". The agents discover two decomposed corpses under the floor who have the same clothes as Mulder and Scully. It's of course one of the ghosts' tricks.
Eating the female eye candy happens in "First-Person Shooter" with the character of Jade Blue Afterglow. She was a very attractive stripper dancer dressed in a scanty silver miniskirt outfit. Every male character, including Mulder, has a major reaction towards her hotness.
Eating the male eye candy occurs in "Bad Blood" when Scully met sheriff Hartwell. She was completely dazzled by his cowboy looks and cute smile.
Eccentric Exterminator: In "War of the Coprophages", a cockroach exterminator opens the episode with a heartfelt ode to roaches before finishing it with "But to them, we humans are gods and should act accordingly" and stomping a particularly unlucky specimen on the floor. It doesn't end well for him.
El Spanish O: Mulder's hilarious "No-ho on the rojo" in "Little Green Men".
Even Evil Has Standards: In "Our Town", Walter Chaco, responsible for the murder and cannibalism of at least 87 people, gives a heartfelt speech about how the town can't turn against its own members or they'd become "an abomination".
Eye Scream. The show had several very squicky examples of this trope.
It's mentioned in "Eve" where the insane Eve 6 says she bit a guard's eyeball, complete with clacking teeth for emphasis. She meant it as a sign of affection...
In "Born Again", creepy girl Michelle keeps disfiguring therapy dolls in exactly the same way. She always gauges out one eye and cut one arm. This is how Charlie Morris's body was mutilated to make it look like a signature execution.
"Die Hand die verletzt" features a human body with a heart and eyeballs cut out. Not coincidentally, Mrs Paddock's desk drawer contains a dissecting tray with a fresh and bloody human heart and two eyeballs.
In the episode "Hell Money" about an Asian gambling ring, losers had to forfeit their own body parts for organ transplantation. We don't see the actual surgeries, but one of the men who was questioned had a fresh gauze-pad on his face, indicating that he'd just forfeited an eye.
In "Unruhe", Gerry Schnauz gave several transorbital lobotomies to troubled women, believing that he was helping them. It used to be known as an icepick lobotomy and it involves inserting a leucotome through the eye sockets. Argh!
The murderous doll in "Chinga" made people claw at their eyes in the teaser. Their faces near their eyes are horribly scratched and one poor guy didn't survive the attack: a knife ended up sticking out of his eye socket.
"Theef" has a voodoo man who sticks two nails through a poppet's eyes that represents Scully which makes her eyes turn completely white and it effectively blinds her.
Facepalm: Over its nine-year-long run, the show had several facepalms of various flavours. *
"Am I the last sane person here?", "I can't believe I did something this stupid", "All right, what next..." or "I might break down completely every moment."
"Syzygy": Mulder rubs his face with a hand when Detective Angela White comes to his motel room and he's not sure exactly what's going on.
"Bad Blood": Scully facepalms when Mulder wants them to compare their accounts of one curious case that involved Mulder sticking a stake into a teen's chest. The facepalm followed his Prison Rape joke about Scully' hypothetical prison mate called Large Marge.
"Patient X": Mulder is among panelists at a UFO conference. Other speakers take the abductions for granted and they enthusiastically talk about "the ontological shock" that must follow. Mulder is looking down, his hands are tightly joined and his thumbs are touching his nose bridge. He's deep in thought, trying to strengthen himself... because he's about to call it all bullshit and blame it on The Government as their their conspiracy.
"Je Souhaite": Scully puts her face in both her hands because she invited some scientists from Harvard to see an invisible body which unfortunately disappeared. She's beyond embarrassed.
"The Truth": Agent Doggett tells Scully that Mulder got death by lethal injection, and understandably, Scully just loses it and heart-breaking sobs escape her uncontrollably. She covers her face with both her hands and continues to cry.
Gas Leak Coverup: The episode "Jose Chung's From Outer Space" features Jesse Ventura playing a Man in Black who tries to persuade someone who saw a UFO into questioning his vision and perception and believing he only saw "the planet Venus".
MIB 1: No other object has been misidentified as a flying saucer more often than the planet Venus. MIB 2: Even the former leader of your United States of America, James Earl Carter, Jr., thought he saw a UFO once, but it's been proven he only saw the planet Venus. MIB 1: If you tell anyone that you saw anything other than the planet Venus, you're a dead man!
Gunman With Three Names: Averted as they are not lone gunmen, but serial killers: Eugene Victor Tooms, Luther Lee Boggs, John Irvin Barnett, Warren James Dupre, Donald Addie Pfaster, Darin Peter Oswald, Robert Patrick Modell, John Lee Roche, and Wilson Pinker Rawls.
The Grotesque: The Great Mutato from "The Post-Modern Prometheus".
Haunted Technology: They loved this trope, though the technology wasn't usually haunted so much as just plain evil. Sometimes it was subverted at the end by implying that there was somebody controlling the device all along.
"Ghost in the Machine" is about an automated security system that develops a murderous mind of its own.
"Blood" has machines telling people to kill. Subverted - perhaps it was the government, using chemicals to cause mass paranoia in a controlled experiment and perhaps some people were actually sending the messages.
"Wetwired" explores a device planted in a TV set sending subliminal signals and inciting the worst fears in viewers. A subversion since it's clear that The Conspiracy placed it there.
"Unruhe" features photography that can capture what's inside people's mind.
"Kill Switch" is similar to "Ghost in the Machine". It's about a software that goes rogue and tries to kill anyone who tries to destroy it. The only way to deactivate it is to insert the kill switch which plays to the tune of The Platter's "Twilight Time".
"First-Person Shooter" has a female video game character in a realistic 3-D game that starts killing people in the game - with effects in real life.
Hate Plague: "Ice", "Syzygy", "Red Museum", "Wetwired" and "Fight Club".
Headdesk: Daryl Mootz in "Rain King" bangs his head on the desk when he hears the sum he's being sued for.
Hemo Erotic: "3" features the sexy vampire Kristen Kilar who licks her own blood and blood of other people. She has some sexually explicit scenes, including the one where she is shaving shirtless Mulder.
Heroic Fire Rescue: Episode "Fire" has two examples. Cecil L'ively successfully attempted to invoke this trope by setting the fire at the hotel so that he could save the boys. It was then played straight with Agent Mulder who rescued the children from the burning house at the final showdown, having to face his paralysing fear of fire.
Hero Stole My Bike: In "Drive", Mulder is forced to borrow an old station wagon. Unusually for the trope, AD Kersh chews him out later for it.
AD Kersh: Compensation to one Walter R. Duncan for unauthorized use of his 1968 Caprice station wagon: $500.
Improbably High IQ: Mostly an inversion of an Improbably Low IQ, in the episode Roland, the title character is portrayed as someone with at least moderate disabilities (eg, can't operate door opening system, limited speech capabilities, passing the time in his group home with young child activities such as stickers), but is said by Scully to have an IQ of slightly above 70, which is in the borderline category like Forrest Gump, and he usually should be indestinguishable in everyday situations from everyone else. It is suggest that he has autism which could account for some of these factors as well as his head rolling, (though he doesn't have most autistic tendencies like problems with eye-contact), but the well-known tendency is for IQ tests to significantly underestimated IQ in people with autism.
I Never Told You My Name: On one episode, a character gives himself away with this trope but he's talking so fast that the audience might not notice until Mulder stops him, saying, "Whoa, whoa, wait a minute here... When did I say my name was 'Agent Mulder'?"
Averted in "The Calusari", "The Walk," and "Home". Also the dog exmaples from "Quagmire" and "Teso Dos Bichos".
Played straight with Baby William, though, at every turn. The number of times that child should have died, before and after birth, are staggering. But not even a scratch.
In Name Only: While not as bad as most cases, the Jersey Devil featured in an early episode is barely anything like the cryptid that's actually reported. It's basically twisted into a poor-man's Bigfoot and dosen't show any of the actual urban myth's notable aspects other than living in the Pine Barrens in New Jersey and the name.
"Grotesque" has a Serial Killer who claims that he's possessed by some dark spirit. Scully thinks he suffers from a dissociative disorder and Mulder informs us that he spent the better part of his twenties in an insane asylum. The episode deals with the issue of spirit possession versus insanity.
In "Chimera", the monster-of-the-week is revealed to have got some kind of dissociative multiple personality disorder: split personality. The woman's overt self was not aware that it was her who was committing the murders.
Intoxication Ensues: Accidental use of substances causing altered and loopy behaviour. The drugs might be administered maliciously. Done several times.
In "Anasazi", the conspirators have been drugging water in Mulder's building to make him irrational and violent. There was a murder due to the drugs.
"Never Again": Ed Jerse's tattoo of a seductive girl named Betty talks to him and forces him to do horrible things. It's revealed that the red tattoo ink was made from rye and contained ergot alkaloid that causes aural and visual hallucinations. Scully got a tattoo as well, but was not affected to that extent.
The vampire from "Bad Blood" drugged Mulder's pizza. He did or did not sing the theme from Shaft.
In "Three of a Kind", Scully is injected with a brainwashing drug to make her forget some evidence she's uncovered, one of its side-effects being the inhibition of higher reasoning. We later see her enthusiastically flirting with an all-male group of defence contractors and The Men in Black. Fortunately, Frohike takes her away, much to their disappointment.
Frohike: Why would the government want to turn Scully into a bimbo?
Inverse Law of Fertility: Inverted — Scully doesn't seem particularly interested in having kids until she finds out her abduction left her infertile, at which point she decides she really wanted to become a mother...and then she inexplicably becomes pregnant.
Type B in the episode "Chimera". Ellen Adderly was horrified as anybody with the murders of her friend and later her rival in their community. At one point she believed she was about to be attacked by the stringy-haired creature she saw in the mirror. It was found out that she suffers from Split Personality and her extreme aggression was how she dealt with her husband's cheating on her.
The copycat killer in "Grotesque" was a leading investigator in the original case. Did he know he was chasing himself? Possibly, as he specifically requested Mulder who he believed is the only one who could crack the case. However, he seems genuinely appalled and distrustful when Mulder reveals to him that it is him who they are looking for. In addition, he then claims as the original Serial Killer that he was possessed by a demonic force.
Lady in Red: The 1939 Scully in "Triangle" wore a gorgeous slinky red dress.
Language Barrier: Employed from time to time, especially with Black Speech languages. When somebody spoke foreign language, the Agents Mulder and Scully were sometimes able to understand as Scully speaks German and is "rusty" in some others, while Mulder claims he had French at high school. The foreign languages were sometimes subtitled for the audience's benefit, but at times viewers were left as clueless as were the characters.
In "Little Green Men": Mulder travels to Puerto Rico to a carefully watched observatory and he meets there Jorge who is very scared and obviously had a weird encounter. Mulder tries desperately to calm him down and question him, but he only manages to produce some broken basic sentences. Finally, Jorge grabs Mulder’s pen and draws on the wall something that looks like a head of an alien with big eyes.
"Nisei": Mulder catches and arrests a Japanese spy who is a part of The Conspiracy. It's not clear whether he could speak English, but he was only yelling at Mulder in Japanese. Mulder also doesn't understand his notes which frustrates him.
Literal Cliffhanger: From "Revelations". An insane businessman grabs a boy and jumps into a paper recycling shredder. When a horrified Scully rushes over, she finds the boy holding onto the railing above the bloody mess.
Literal Surveillance Bug: The robo-roaches from "War of the Coprophages". It's implied that rather than spy gadgets, they're actually space probes sent to explore the Earth by a far-off alien civilization.
The killer in "Grotesque" is eventually revealed to be a profiler who looked too long into the abyss of a particular serial killer and turned into him. Whether this is a psychological effect or transferred demonic possession is left up to the viewer.
The possibly demonic serial killer and necrophiliac Donnie Pfaster from "Irresistible" and "Orison".
Medical Horror: Happens often enough during the Myth Arc episodes, but taken about as far as possible (for prime-time TV, at least) in "Sanguinarium," which takes place in a hospital and features death by liposuction, death by plastic surgery and various other horrifying scenes.
Mocking Music: In "Vienen", Agents Mulder and Doggett are pursued by oil rig crew members who have been infected by the black oil. They are violently banging on the door of the communications room, while Doggett tries to get the radio working. The static changes to The Ride of the Valkyries.
Money, Dear Boy: The in-universe reason Jose Chung writes his bestselling novel From Outer Space.
Motion Blur: "Rush" has a key plot-point where security footage at a high school was found to show a strange blur. Using experimental technology to colorize it, the agents reveal the blur is made up of the school colors, suggesting that it comes from the jacket of one of the (superpowered) students.
Multi-Part Episode: There are almost as many multi-part episodes of the show as there are stand alone. Most of the mythology episodes ended up being multi-parters though they were rarely named as such.
Mundanger: Loads — mass panic in "War of the Coprophages" (subverted in that there really are robotic alien cockroaches involved, but they have nothing to do with the deaths in the episode); serial killers in "Grotesque", "Orison" and "Irresistible"; one really nasty family in "Home"; organized crime in "Hell Money"; a Cannibal Clan in "Our Town"; an alligator in "Quagmire."
Murder by Cremation: "Hell Money". A gambling ring among Chinese immigrants claims organs as collateral; if you can't pay up (or if you rat), you're disposed of in a crematorium. Alive.
Murder by Mistake: Melissa Scully is shot instead of her sister in "The Blessing Way".
Murder Suicide: In "Demons", Mulder's weapon has been used in a crime and he doesn't remember what happened. He's arrested, but it's revealed that the couple's death was a murder-suicide, and Mulder's released.
In the episode "Fallen Angel", it's implied that aliens are responsible for Max's epilepsy.
In "E.B.E.", Mulder suggests that Gulf War syndrome is the result of alien encounters.
A notable episode featured an adult with Pervasive Developmental Disorder (also referred to in the episode by its old name, "Atypical Autism"); he was portrayed quite realistically despite his connection to the paranormal.
New Years Resolution: Scully has a good one in "How the Ghosts Stole Christmas" - apparently it's not to follow Mulder on all his crazy off-side projects.
No OSHA Compliance: In "Beyond the Sea", the climactic chase scene takes place in an abandoned brewery that is falling apart. The villain steps through a wooden plank bridge and falls several floors to his death.
"Home": Scully to Mulder who is a bit spaced out and playing with a baseball.
Scully: Meanwhile, I've quit the FBI and become a spokesperson for the Ab-roller.
"all things": Mulder to Scully who is preoccupied with her salad.
Mulder: And I'm not wearing any pants right now.
Not So Stoic: Scully gets several of these moments — the best example is probably "Irresistible," where she finally realizes Mulder won't think any less of her for seeing her break down after a traumatic experience.
Not The Nessie: "Quagmire" has Mulder and Scully investigating reports of a lake monster. In one scene the owner of the local tourist trap is shown faking some monster footprints, whereupon he gets eaten by the real monster, a large alligator. However, the audience can see there really is a giant serpent in the lake.
Nubile Savage: "The Jersey Devil". Her legs were rather smooth for someone living in the woods of Jersey.
Nuclear Nasty: Flukeman from "The Host" is a monster created by radiation.
Eugene Victor Tooms from "Squeeze" and "Tooms" was a genetic mutant and Serial Killer who needed human livers to hibernate. He looked to be in his late twenties in 1993, but his first murder had occurred in 1903.
Origins Episode: "Musings of a Cigarette Man" for C.G.B. Spender, "Unusual Suspects" for the Lone Gunmen.
Out-of-Character Moment: Played in-universe; the phenomenon in "Syzygy" causes not only Mulder and Scully to act in ways they normally wouldn't, but also apparently the entire town it's focused around; the normally calm and rational high school principal turns into a ranting fundamentalist nutcase, for example.
Papa Wolf: Howard Graves in "Shadows". Do not mess with his secretary/surrogate daughter even after he's dead.
The Peeping Tom: "Red Museum" features a man who secretly records everyone living in his building from inside their bathrooms.
Mulder gets very frustrated in "Bad Blood" and he gives full vent to his anger in kicking the hell out of a trash can violently. (He killed a teen by jamming a wooden stake in his chest and the FBI is being sued for $446 million dollars. Anyway, Mulder had been drugged.)
In a less humorous example, in "Sein Und Zeit" Mulder reacts by attacking his desk when Scully tells him that his mother committed suicide.
In "Anasazi", Mulder thinks he received a fake tape with "gibberish" instead of top secret government files. He hits a pencil holder and smashes it against the wall. But the files are actually encrypted. Poor Mulder has been being drugged, so he ends up punching Assistant Director Skinner a moment later.
"Wetwired": Mulder is on his way to identify a body which might be Scully. The messenger of his jerk of an informant follows him and insists that he keeps investigating the case, yet still gives him only super vague leads. Utterly frustrated, Mulder kicks the door of the Plain-clothed Man's car.
Pinocchio Syndrome: "The Unnatural" has an alien who became a man thanks to his love of baseball.
Nanomachines: The cause of Skinner's poisoning in "S.R. 819".
Phone Call From The Dead: In a Myth Arc episode, Scully gets a phone call from her dead sister. This ends up leading her to a girl who is her biological daughter, created using the ovum extracted from her body.
Prisoner Exchange: Mulder performs such a trade in "End Game" between Scully and an alien clone he believes is his sister Samantha.
Reality Writing Book: In "Milagro", a writer moves in to Scully's apartment building and starts affecting her life with his writing.
Reality Subtext: In "Hollywood A.D." a film producer decides to make a movie based on Mulder and Scully's adventures, casting Garry Shandling and Tea Leoni for the roles, respectively. Scully mentions to Mulder that Leoni may have a crush on him, which he considers ridiculous. Any guesses to whom David Duchovny is married in real life?
In "The Field Where I Died", Mulder comes to believe that he was married to a female member of a cult in a past life, and under hypnosis claims to remember not only her but Scully, Samantha and Cancer Man as reincarnated friends and enemies respectively.
In "Born Again", a cop was reincarnated to a little girl. When she was eight, the revenge on the cop's murderers was on.
The character who swore revenge came back as a fly in "The List".
Reminiscing About Your Victims: A villain of the week attempts to convince Mulder that he killed Mulder's sister by doing this. Mulder eventually call bullshit on him.
A Riddle Wrapped in a Mystery Inside an Enigma: The episode "Patient X" contains a variant on the trope phrasing. Agent Mulder, who has grown skeptical of the existence of extraterrestrials but instead believes the alien conspiracy to be a lie concocted by the military to hide a different and all the more sinister scheme, describes his belief in "a conspiracy wrapped in a plot inside a government agenda."
The Conspiracy Theorist who believes in aliens and who wants to be abducted in "Jose Chung's From Outer Space" has a corner in his room which is a nice foil to Mulder's office. He even has a similar poster but the message reads "I believe".
In "Grotesque", Mulder sinks deep into ugliness and madness of the case. At one point, the walls of his apartment are completely covered with gargoyle sketches. Mostow's studio also counts.
Mulder reveals in the episode "Hollywood A.D." that he's seen Plan 9 from Outer Space forty-two times. He claims that the sheer badness of the film numbs his brain, allowing him to make intuitive leaps and solve problems that have him stumped.
Scully: You've seen this movie 42 times? Mulder: Yes. Scully: Doesn't that make you sad? It makes me sad.
In an earlier episode, the agents ran across a woman who was convinced she'd been impregnated by Luke Skywalker. This becomes even more hilarious when it is revealed she's seen Star Wars 368 times, and was hoping to break 400 by Memorial Day.
Serial Killer: Several times. Most of them are really horrifying.
Series Fauxnale: Season 7's "Requiem" was designed to be the series finale. Mulder and Scully return to the site of their first case together, pretty much every major character gets an appearance, and the episode ends in true X-Files fashion in which Mulder is abducted and Scully finds out she's pregnant without conclusion or explanation for either. A lot of fans treat it this way, since many regard season's 8 and 9 as subpar to the rest of the series.
It takes place in the town of Miller's Grove, a twisting of Grover's Mill, where the Martians first land in Orson Welles' radio version of The War Of The Worlds (foreshadowing the fact that the only thing that actually poses any danger in the episode is mass hysteria).
In one of Doggett's first episodes he's skeptical of a case about someone being able to see through walls, so he comments "Calling Clark Kent."
The scene in "One Breath" where Mulder goes to the CSM's apartment is basically a re-creation of the scene on The A-Team where Murdock gets onto Stockwell's private jet. They're both faced with the possibility of losing someone they care about (for Mulder it's Scully, for Murdock it's the rest of the team), they both get access to a powerful, manipulative man who is supposed to be untraceable, burst in brandishing a gun, and demand information. Also, both are met with a calm, unfazed response from said powerful men.
"Hungry" gives this to the Monster of the Week, who is just trying to get by and live with the trouble his power/affliction causes. Mulder and Scully don't appear until the end and then they shoot him.
"Musings of a Cigarette-Smoking Man" gives one to CSM.
Subverted in "Rain King". Mulder and Scully have to share a hotel room with just one bed. They're kind of annoyed over the hotel assuming they wouldn't mind sharing a room, but no real tension or embarrassment between them comes of it.
Played just a little straighter in "Arcadia", where they're undercover as a married couple. Mulder has some fun teasing Scully by suggesting that she get in bed with him, but it's still not treated like a big deal.
Scully: First of all, Mulder, if the family of Ronnie Strickland does sue the FBI for, I believe the figure is 446 million dollars, you and I will almost certainly be named co-defendants. And second of all... I don't even have a second of all, Mulder. 446 million dollars.
Title Drop: In the episode "Travelers", it's explained unsolved cases were filed under "U", until space in the filing cabinets ran out, so they were then put under "X" which had extra room. Thus, the unsolved cases are "X" files.
Toad Licking: The episode "Quagmire" had a bunch of slackers licking toads to get high.
Snorkel Guy: Dude, what is wrong with you? You made me drop my toad!
Scully almost died of alien-induced cancer. Other abductees were not as lucky.
In "Leonard Betts", the Monster of the Week was a man made entirely of cancerous tissue. He could regenerate the loss of his head and had to eat cancerous tissue removed from surgery patients (he worked in a hospital). Mulder and Scully squicked in-universe when they found out.
Totally Radical: In "First-Person Shooter" and "Kill Switch." Doubly unforgivable as both episodes were written by cyberpunk authors William Gibson and Tom Maddox, who should know better.
Creepy Blue Eyes: John Barnett's blue eyes were glassy and glazed over, and they appeared dead. Even the pupils were blueish.
Hellish Pupils: Animal-like pupils were used for a satanic demon in "Die Hand die Verletzt", then for a South American Indian shaman in "Teso dos Bichos" and for a demonic woman in "Terms of Endearment".
Uncanny Village: "Arcadia" features a seemingly peaceful American-dream community controlled by Home Owner Association, represented mainly by President Gene Gogolak. They have strict rules and regulations about everything and observing them is enforced by death threat.
In "Leonard Betts" — "I'm sorry... but you've got something I need."
In "Clyde Bruckman's Final Repose" — "How do I die?" "You don't."
What Happened to the Mouse?: Mulder wears a wedding ring in "Travelers", which is set just a year before the start of the main plot. Of course no reference to him ever being married occurs anywhere else. And when there is his profile on screen, his marital status reads "single" or "unmarried".
Mulder suffers from pyrophobia, and guess what? He has to face it in "Fire". It's fair to note that it was not accidental as Phoebe Green requested his help on the case and she knew about his fear.
Subverted with Agent Scully. In "One Breath", her mother tells a story how she felt guilty for shooting a snake with her new BB gun. Although deathly afraid of snakes, she held the snake and it died in her hands. When Mulder and Scully investigate cases involving snakes, she isn't exactly on edge ("Die Hand die Verletzt") and she even gets a tattoo of a snake eating its own tail in "Never Again". On the other hand, there are lots of snakes in "Signs and Wonders", but even Mulder who doesn't suffer from this phobia is very nervous around them.
All the perpetrators in "Blood" were phobic and the exposure to insecticide heightened their already existing phobia to an unbearable level. One killer was claustrophobic (Why did it have to be a crowded elevator?), another one had a paranoia about rape (Why did it have to be a mechanic in a garage at night?) and the last one was Afraid of Blood (Why did it have to be blood?).
Scully's abduction — an event that would go on to shape the entire Myth Arc, as well as Mulder and Scully's relationship and Character Development throughout the rest of the show — was written in simply to get Gillian Anderson out of the way while she was heavily pregnant in Real Life.
There are also several more episodes where either Mulder or Scully are mostly absent while their actors were off doing other things — especially in season five, while they were filming the first movie.
In "Fearful Symmetry", the Lone Gunmen appeared, but Langley was absent. The real-life reason? Dean Haglund was booked to appear on a Sliders episode ("Fever"), which was filming at the same time.
Larry Musser appeared on the show four times. He was Sheriff John Oakes in "Die Hand die verletzt, Detective bleeping Manners in "Jose Chung's From Outer Space", ex-marine in Denny Markham in "Unrequited" and PD Captain Jack Bonsaint in "Chinga".
Terry O'Quinn as a three-peat. First he played Lt. Tillman in "Aubrey", then bomb expert Darius Michaud in Fight the Future, and finally one of the Consortium in "Trust No 1".
Chris Owens also appeared several times as a young Smoking Man before being cast as Agent Spender. Considering the two characters' relation as father and son, this was likely intentional.
The trio of stoners in "War of the Coprophages" turn up again in "Quagmire".