* At the joint U.S. military/FBI sham trial in series finale "The Truth", telepathic mind reader Gibson Praise is called in to offer defense for Mulder, affirming that he indeed can read people's thoughts. The judges panel is shown blinking confusingly while the prosecutor looks incredulous and then it just moves on. Alright... But then later, Agent Reyes testifies that Scully's Baby William demonstrated telekinetic powers and the prosecutor baits her to produce the child to prove these powers, something she cannot do as the baby was given up for adoption by this point of course. So why didn't the prosecutor ask for a demonstration of Gibson's telepathy then? It shouldn't have taken too much convincing. And why didn't Mulder's defense give that demonstration, which would have been a clear example of the paranormal and provided at least some incontrovertible evidence for their claims? Even if they were trying to protect Gibson, he had already voluntarily exposed himself to protect Mulder, so proving his powers was the next logical step in defending his testimony. Yet this isn't even considered? Unbelievable. Seems like just another arbitrary way the writers could [[FailureIsTheOnlyOption prevent Mulder and Scully from actually presenting the proof they worked so hard to uncover]], but in this case the failure to even mention it drives it in to clear WallBanger territory.
* Not really a complaint, having watched only five episodes, but how do the rest of the FBI (or other government agencies) handle the information on AliensAndMonsters and A.I. and blahblahblah...
** It's probably handled the same way as all odd claims. Forgotten, covered up, and thrown away.
** Or just toss it in the basement and let that weird guy down there take care of it.
** Many episodes close with more immediate legal concerns: just for one, "Schizogeny" ends with a local weirdo beheading the episode's villain, who to all outward appearances is an upstanding therapist. I wonder how the inquest went.
* Why does Mulder always drop his gun? It seems like every single time he confronts the alien/monster/mutant of the week he always drops his gun. It always made me wonder why he even bothered to carry the stupid thing.
** Rule of Drama, probably.
** This is actually lampshaded in the episode Nisei, where Mulder is kicked to the ground, disarming him in the process. He then proceeds to whip out his throw-down (a back-up pistol in an ankle holster). Mulder even states he got this because he "got tired of losing his gun".
*** He also used the back-up gun in "Paper Hearts".
** He has to carry it; he's an FBI agent. They carry guns even off duty.
* Speaking of guns, there is a mention on ArtisticLicenseGunSafety page that Mulder and Scully are shown following the appropriate rules for law enforcement most of the time. But several times somebody manages to take their gun or as noted above, Mulder loses the gun somehow. Sometimes they take the appropriate measures, but at times they aren't really worried that somebody might use it and make them responsible for possible murders. One of the worst examples happens in "Demons", where Mulder's gun was used in a murder/suicide. Mulder couldn't remember anything so he was arrested and interrogated. Obviously, he didn't do it and wasn't charged, and he was also drugged because of some psycho treatment. But how come he wasn't charged for losing his gun and negligence in this case? Aren't law enforcement people responsible for their lethal weapons or something? Mulder doesn't even get a WhatTheHellHero speech from Skinner.
* There's a 5th season episode, "Travelers", that's always bugged me. A man in the 1950's had been surgically grafted with a spider-like creature that lived inside him and crawled out of his mouth and [[OrificeInvasion into other people's mouths]] to eat their internal organs, making him a BodyHorror vampire thingy who angsts over his condition. But the spider's not physically attached to him. And when they did an autopsy of another man who killed himself after the procedure was done to him, his spider-thingy was still alive. So... why doesn't he just ''walk away'' when his pet spider's crawled out of his mouth and is doing its digesting thing? The episode always cut away as the spider was emerging and crawling back in, so we never really saw how that works. He doesn't need it to stay alive, and it apparently doesn't need him either (it survived for days inside the other guy's body). Does the host go catatonic or something? Is his brain somehow linked with it so that he needs it to be conscious? But this was the 1950's, and the episode described the experiment as gruesome, fairly primitive grafting surgery done by former Nazi doctors. It's a minor plot point in a MonsterOfTheWeek episode, but I still can't figure it out.
** Okay, now that I think about it, maybe he could be a little more heroic and grab, capture or just squash the spider thing rather than just running off, but still... for that matter, what would've happened if one of his victims had managed to throw the thing away, or trap it under a box or something?
* The episode "Calusari" really is starting to bug this troper. Why is the grandmother so secretive about all this? Why don't the Calusari explain? Why doesn't Charlie's mother simply overrule her son and actually talk to the doctors? The whole thing is almost like an episode of RescueMe when it comes to bad decisions!
** Who would have believed the grandmother, or the Calusari? That would just sound like crackpot superstition to most people. As for why the mother doesn't talk to the doctors before she takers her son home...yeah, I got nothing. That was just dumb on her part.
* Scully's skepticism about aliens is established in the pilot when Mulder asks her "Do you believe in the existence of extraterrestrials?" Scully answers "Logically, I would have to say no. Given the distances need to travel from the of reaches of space the energy requirements would exceed a spacecraft's capabilities." Which is a valid point, but it doesn't answer his question. He's asking her if she believes in life on other planets, not if aliens are interfering with this one.
** She does clarify this later, in "War of the Coprophages", when she says she finds the idea of life on other planets in general too far-fetched, as life on ''this'' one came about because of a very unique sense of circumstances unlikely to occur anywhere else.
*** Also a valid point, but the question remains -- why does she answer one question with the answer to the question he didn't ask?
** I just assumed that she just assumed that, given his reputation, his interest in the paranormal and the basic ''raison d'ere'' of the X-Files office to begin with (investigating weird things happening on Earth, not other planets), she rationalised that he was either building up to outright asking "do you believe that we've been visited by extraterrestrials?" or assumed that he was just asking her that in a coded fashion anyway (particular given the slightly dramatic way he frames the question) and decided to cut that line of conversation off before it started. Which is still dodging his actual question, I guess, but she's letting him know from the start that she's skeptical about him and his work.
* The fact that Mulder and Scully aren't very good at actually ''doing'' anything to close their cases. They usually ''figure out'' what's going on, or at least advance a theory that's basically correct, but half the time the monster has already either killed a bunch of people or survives the end of the episode, which makes one wonder what happened after they've left the area. Did the fluke man in "The Host" just...stop killing people, or leave? At the end of "Ghost in the Machine," the AI is clearly still alive, looking right at the jerk FBI agent who tempts fate by saying "I'm gonna figure this thing out if it kills me!" Did the AI just change its mind? Two of the inbred hicks in "Home" got away, and it's pretty much stated outright that they're going to start again somewhere else. You'd think Mulder and Scully would pay more attention, unless the monsters of the week who aren't quite dead just stop killing people and mysteriously vanish.
** Yes, these TheEndOrIsIt endings bear some serious FridgeHorror if you think about it.
** But, wouldn't you say that being unable to completely close cases is a theme--not in those exact words, but think about? When there are only two people trying to solve the mysteries of the world and dozens of other people trying to keep them quiet, what do you do? Despite, the open-ended cases, they realize that if it weren't for them, those people have no one. Even if it isn't absolute closure, there are still answers. It is scary that some of these monsters are still alive and kicking, but Mulder and Scully can only do so much--they are superheros and they don't have all the answers.
*** Exactly. Plus, watch each Monster of the Week episode. I like to try and figure out what would have happened if Mulder and Scully hadn't been there. Quite often, even in the times the Monster gets away, the pair do save lives! There would often be many more deaths if they hadn't shown up. You reference Home - that still means that only two of them got away. Mulder and Scully do make a difference, just...as much as two people with all odds stacked against them can.
*** The more intelligent of them also probably decide to go (even further) underground having attracted the attention of the FBI.
* I'm really confused about "Ice". How did the lady who ends up infected with the parasite get infected? Mulder was attacked by the infected dog (though it didn't break the skin), Scully and the one doctor were exposed to infected blood, and the geologist was handling the ice cores. How was she exposed? When?
** It's based on ''Film/TheThing1982''. In that movie, the audience doesn't get to know who is infected and how they got infected, either (at least for some characters). That's the whole point, and greatly amplifies the horror. [[spoiler:At the end, you really don't know if the last two survivors are infected or not.]]
* My major mystery of the last two seasons: did nobody working on the show realize that the alliterative words "super soldiers" sounds really silly when said over and over and over again? "So-called super soldiers" is even worse!
** Maybe it was for the AddedAlliterativeAppeal. So-called super soldiers sound so sexy! Seriously!
* In "Fallen Angel", where does Mulder get the sudden knowledge to criticize the cover-up team's tactics? For all he knows this alien is the extraterrestrial equivalent of a serial killer and hunting it down is the reasonable reaction.
* So, in "The Post-Modern Prometheus", it's revealed that the tragic monster and his adoptive father were basically raping and impregnating women with mutated children to get the titme figure a "mate", which is THE EXACT SAME THING the conspiracy does, but while the father and son are seen as tragically misplaced and get forgiven, the conspiracy is seen as complete monsters. Uh... WTF?
** Yes, it's really weird that the women don't feel violated. The lady who called Mulder did at least a little bit. But the evil scientist's wife was shown to be very excited about the possibility of being pregnant. Sure, we were told she really, really wanted to have a baby, but like this? With a monster or animal sperm/embryo? Seriously. But the end is only a piece of post-modernistic story-telling, which means it didn't actually happen, and therefore the monster was probably arrested and prosecuted.
** Fairly good explanation for this head-scratcher appeared in one review on the imdb. The Mutato reveals the truth behind the mysterious impregnations, explaining that it was his father Old Man Pollidori who had been inseminating the women of the town with mutated DNA that was fused by his own farm animals. There are several hints that Mrs. Berkowitz's son Izzy is close to a pig and the reporter to a chicken. But then it's a weird thing to say that the old man was not successful because he was, only too much! Mutato did act as an accomplice to the crimes the Old Man commit, but any charges against him would be dropped in American court by reason of mental disease or defect, being that he had spent his life in isolation and was psychologically impaired from making informed decisions. Mutato did not believe he was doing anything wrong. He was dancing along to Cher and eating the peanut butter of the houses that the Old Man broke into. He has the mind of a child and even made a statement of being incapable of wrongdoing. The Old Man received justice for unlawfully fertilizing these women against their knowledge with the capital punishment - death. Dr. Pollidori was arrested for killing his father. Mutato's dream of meeting Cher came true. Everyone got exactly what they deserved.
* Who is really the biological father of the Mulder siblings? Sometimes it's subtly or not so subtly implied that it's the Cigarette Smoking Man. He's Mulder's father, then he isn't, then he's in fact Samantha's father. Or did he father them both? Why didn't somebody do the freaking DNA tests? Doesn't Mulder want to know? Oh, and he's also Agent Spender's father. How many women did the Cancer Man make pregnant?
** The ambiguity is, to be fair, kind of the point. As for why Mulder doesn't find out conclusively one way or another, well, the Cigarette Smoking Man doesn't exactly make himself available for DNA tests and Mulder isn't exactly fond of him -- chances are, he'd rather ''not'' know if he could help it.
* How could Scully give up her son? How could she think it could help him to have a better life? It doesn't make any good sense. It can't be so very hard for the omnipotent conspirators and colonists to track the baby down. If anything, William's life is more endangered because at least his biological mother and The X-Files gang knew about the threat. Now what happens if they find him and he has only the ignorant adoptive parents to protect him? [[hottip:*note:According to TheOtherWiki, the idea for Scully to give William up for adoption was mandated by Chris Carter and Frank Spotnitz. David Duchovny (credited for co-writing and directing "William"), Gillian Anderson, and executive producer John Shiban were not happy with this turn of events, due to them being parents and feeling that the action was not realistic, but "grudgingly consented".]]
* From the first movie: How the hell did they get from Antarctica to Washington D.C.?
* In one of the multiple times that Alex Krycek reappeared after a long absence or being presumed dead, there was a scene with him dipping a tea bag while having a plastic/prosthetic hand. It was never mentioned in the scene or ever again on the show. He had two normal hands in all appearances after that episode. And that scene was used as a clip in "The Truth". So, what was the deal with that hand? I initially thought it was just weird for the sake of weird, but then I figured it was just another aborted idea. But it's really weird and has been bothering me.
** Krycek's left arm was amputated in the 4th season episode "Terma" and his prosthesis was actually shown a few times in later episodes (such as when he was killed by Skinner). Ultimately it seemed significant only to his characterization (RedRightHand; PhysicalScarsPsychologicalScars; GoodScarsEvilScars; etc.) and not the plot.
* In the penultimate episode of the series, "Sunshine Days", Oliver Martin has the ability to change his surroundings (and that of others around him) with his imagination. It mostly manifests in him reimagining his house as the Brady Bunch house, complete with Alice and the family. Once the agents find out about this, they over look the fact that he was directly responsible for the deaths of two young men who entered the house. Granted, they were intruders, but he shot them through his roof and hundreds of feet away. But they look over that because Scully wants to study his brain, feeling it is the proof and vindication she and Mulder have been looking for on the X-Files. How much more proof did Scully need to believe in that kind of stuff? Even if you disregard all the monsters, aliens, freaks, and the over all insane things that happened to both Mulder and Scully, in the very next (and last episode), A.D. Skinner states that the abilities of Gibson Praise have been scientifically and unequivocally proven to be true. So, was Gibson's scientifically proven abilities that she scientifically proved herself not enough for her to believe in the X-Files? That whole thing stuck me as bizarre that after all she had been through over 9 years, this case was the one that would justify her beliefs.
** Hmm, 'tis true that she acquired some proofs over the course of the series, apart from Gibson Praise the guy turned invisible from "Je Souhaite" comes to mind. Scully was really excited for that one, and she even called some scientists from Harvard, and embarrassed herself over it. The thing is, the proofs were often stolen or they disappeared, or the conspiracy made them disappear, no? They seriously threatened or ridiculed people who tried to expose some of the stuff, too. In "Empedocles", Scully owns that she was always afraid to believe, which sounds like one of the points in the series which shifted Scully from a sceptic to a believer. And finally, Oliver Martin was possibly only indirectly responsible for the killings. It seemed it was not his intention to do kill those guys, and he almost injured Doggett and said he didn't mean to, because he wasn't always able to control his powers.
* Where are the serious journalists and media people in the X-Files universe? Mulder and Scully sometimes do get their proof of the paranormal. For instance, the proof of a fifth and sixth DNA nucleotide from "Erlenmeyer Flask" or the freaking Flukeman from "The Host", or the parasites from "Ice" or "Firewalker", or the extreme and possibly destroying science from "Ghost in the Machine", "Young at Heart", "Soft Light" or "Post-Modern Prometheus". Why isn't there anybody who would write about the cases? How come only the Lone Gunmen or tabloids (one magazine cover in "Pusher" did feature the Flukeman) were interested in publishing them? Yes, in some cases the evidence was destroyed and the people involved threatened by the government or the conspiracy, but not always. A spunky and intelligent [[IntrepidReporter reporter]] might be Mulder and Scully's useful ally in revealing the truth to the general public. The only problem was probably that ''trust no one'' thing.