* AcceptableTargets: In general, the show is fond of making the victim a member of a particular subculture, then wildly exaggerating said subculture, making the members of that subculture look like ammoral assholes, freaks, morons, etc.
** Congressmen and lobbyists.
--->'''Brennan''': If we're buried more than 4 feet deep, the concussion will turn our brains into jelly.
--->'''Hodgins''': Well, then we can run for Congress.

--->'''Sweets''': A "corruptor" would mean a herectic, like, say, a pretender to the throne.
--->'''Sweets''': A lobbyist? Oh, that's a ''total'' pretender to the throne.
** People on the Internet in "The Woman in the Whirlpool". This example, while rather subtle, might not be too much of an exaggeration...
--->Have you even been on the Internet? It's the land of nasty, bitter people.
** It would seem as though no one in England has even heard of a decent cup of coffee.
* AlternativeCharacterInterpretation: Angela's dad. His revenge on Hodgins is to get him drunk, tattoo him with Angela's face on his arm, then leave him in the desert. The fact is, he could have done far worse things, though getting him drunk and leaving him out in the desert is not good, the tattoo... is he secretly an Angela/Hodgins ShipperOnDeck and thought the break up would be temporary?
* ArcFatigue: Pelant. He appeared on the middle of season 7 and was only caught early on season 9, being around for far longer than any other recurring serial killers. The writers really seemed to like him, as they put a DiabolusExMachina at the end of the Season 8 premiere for the sole purpose for having him hanging above the team's heads for another season. Many fans accused him of being a CreatorsPet, and rejoiced when he finally was [[spoiler: killed by Booth.]]
* AuthorsSavingThrow:
** [[spoiler: Zack Addy. Early on in season 4 he reveals to Sweets that his killing of the lobbyist was only MetaphoricallyTrue, and [[CharacterRerailment he hadn't actually committed the murder]]. This makes Zack's only crime being an accessory to murder]].
** After Pelant [[spoiler: coming in between the engaged Booth and Brennan]] in the Season 8 finale ignited fans' rage, the writers decided to quickly wrap up the plotline, [[spoiler:killing off]] Pelant in episode 4, and having Booth and Brennan tie the knot in episode 6.
* BaseBreakingCharacter: Pelant. Either he's one of the best and most dangerous {{Big Bad}}s ever on the show, or he got way too much screentime and was treated as a nigh-omniscient force. There's plenty of room for both sides to make an argument.
* BadassDecay: In the first couple of seasons Brennan is presented as a capable and skilled martial artist. This seems to have been abandoned in later seasons, noticeable in "Harbingers in the Fountain" where an untrained doctor clumsily wielding a simple scalpel is more than a match for her.
** In Season 7's ''The Warrior in the Wuss'', she provides some significant information about Karate, and just about any self-defense instructor will tell a student that just because someone is untrained doesn't mean they're not a significant threat, ''especially'' if they're armed and/or highly motivated. Even in the first episode, she was perfectly willing [[spoiler:to shoot a guy threatening to burn both of them to death instead of trying to subdue him.]]
** She's back to taking out three guys at once in the season 6 opening, so this is likely a case of DependingOnTheWriter.
* CompleteMonster:
** The Gravedigger, aka [[spoiler:[[KillerCop Heather Taffet]]]], is a dark cross between a SerialKiller and a serial kidnapper. Their modus operandi is to sneak up on victims, knock them out with a custom-made stun gun, and bury them in a hidden container with 24 hours of air; either the ransom is paid, or the victims die. The Gravedigger's introduced by doing this on Dr. Brennan - not because Brennan is a threat, but just because. The Gravedigger also traps Dr. Hodgins at the same time (cutting the available air to around 12 hours) just because he witnessed the kidnapping. When reappearing, The Gravedigger then tries to similarly bury Booth alive to destroy evidence, plus tries to kill Brennan and Booth again. The Gravedigger also kills a private investigator with her stun gun because The Gravedigger thinks that there's a chance that he might find The Gravedigger in the future. Several of the other victims are also sought, with the cruel circumstances behind them all played up. In the end, The Gravedigger admits to [[ForTheEvulz just enjoying killing people]] and the effects that BuriedAlive has on victims; the ransom money was immaterial.
** Christopher Pelant, from seasons 7 to 9, is a [[HollywoodHacking genius hacker]] and a brutal SerialKiller. His first murders his guidance counselor after forging a recommendation for him to go to Stanford. In his adult life he was under house arrest for hacking UsefulNotes/ThePentagon; he later escapes and retaliates against the government with a new killing spree. Always one step ahead of the Jeffersonian team, Pelant is not afraid of using brutal tactics against them, and proudly takes responsibility for his actions. Pelant would later [[FrameUp frame Brennan]] for the murder of a friend and pulls strings to keep her friends from interfering. In a later appearance, he [[SadisticChoice forces Hodgins]] to forfeit all his money or else he'll [[WouldHurtAChild destroy a girls’school]] in Afghanistan with a military drone. He also cripples and later kills FBI agent Flynn, and brainwashes a girl into killing three FBI agents. When he [[StalkerWithACrush develops an intellectual infatuation with Brennan]], he coerces Booth into calling off their wedding, and not to tell her why, or else he'll continue to kill innocent people. When finally cornered in his hiding spot, Pelant takes to holding Brennan at gunpoint in a last desperate attempt to win. Intellectual, [[ItsAllAboutMe egotistical]], controlling and vindictive, Pelant proves to be a dangerous enemy to the Jeffersonian team with his love for playing people like pawns, and killing those in his way.
* CrazyAwesome: Angela's dad. Let's list the things he's done.
** After Hodgins and Angela broke up, he got Hodgins drunk, gave him a tattoo of Angela, and left him in the desert.
** He asked Hodgins to retrieve the car he lost in a poker game from the bikers who took it.
** He insisted that Hodgins and Angela had to name their baby Staccato Mamba. When Hodgins refused, he got Hodgins drunk and gave him a tattoo of himself (imagine having a tattoo of your wife on one shoulder and her father on the other), as a way of congratulating him on standing up to his father in law.
* CreatorsPet: Pelant. The writers really seemed to enjoy writing him, as they used at least one AssPull just to keep him one step ahead of the Jeffersonian team.[[note]]The Pelant saga feels like it was originally going to end with "The Future in the Past", but instead the crew decided to keep him around for another season.[[/note]] Fans however got annoyed at Pelant being built up into an overpowered InvincibleVillain. He was given the role as the main antagonist of ''two'' season finales, and other characters were also very quick to call Pelant brilliant and even say that he's smarter than them. Ultimately, however, the writers made the right call and finally ended him early on in Season 9.
** ...Though this didn't stop them from repeatedly mentioning the guy during the subsequent Ghost Killer arc, and bringing him back for both the 200th episode and the Season 10 finale.
* CriticProof: This show was, in the words of the crew, FOX's "little show that could". Many critics and reviewers brushed it off as yet another procedural (completely ignoring that it's more character-centric than others), FOX themselves walked a thin line between "taking it from granted" and "forgot it existed", also going on to move it all over the schedule. ...And yet, despite never really getting much recognition, the show found an extremely loyal audience that helped it survive for 246 episodes over 12 seasons.
* CriticalResearchFailure:
** In ''The Twist in the Twister'', it's clear little to no research was done on severe storms. To start with, when a body is discovered to have been deposited by a tornado, the investigators [[FailedASpotCheck completely neglect to check the path and rating of the tornado.]] Worse, the storm chasers themselves are grossly incompetent, with their leader stating that a mesocyclone in an already developed supercell is only just forming, when in fact a tornado is mere moments away from touching down. One character--who happens to be in the third trimester of pregnancy at the time--drives ''into'' the tornado and makes it without a scratch because she [[DoNotTouchTheFunnelCloud didn't touch the funnel itself.]] Finally, minor debris strewn across unmoved and otherwise unhurt vehicles leads the storm chasers to conclude that the tornado was at least an [=EF4=]. Oh, and how does one get a full rainbow against a clear blue sky instead of a retreating thunderstorm, anyway?
** Possibly a case of RealityIsUnrealistic; in the episode ''The Bullet in the Brain'', Bones mentions that Booth holds the world record for longest confirmed sniper kill at around a kilometer (she says it was slightly less, he says it was more). In real life, there have been no less than ten confirmed sniper kills at more than a kilometer, several at twice that range, and every one of them was made years before the episode aired.
** In ''The Passenger in the Oven'', one of the old ladies who reads a lot of murder mysteries and is generally portrayed as being a reasonably well-informed amateur detective claims that most murder victims are women. This is not even remotely close to the case: male victims outnumber female victims by a factor of 3 or so (although it varies slightly by jurisdiction).
** See Narm for more on this. The Norwegian in the episode ''[[Recap/BonesS4E21MayhemOnACross Mayhem on a Cross]]'' is clearly not written by someone who knows the language very well, and is seemingly more English put into Google Translate. There are more than enough Norwegians in the business, or you know ONLINE, they could've asked for help. Even the Norwegian actor in the scene! The Norwegian police acts nothing like their real-life counterparts either. So in the end it's just kinda the glorification some republicans wants to return to when rights for someone else than themselves is mentioned. Well, it's FOX so...
** Someone in the writers' room clearly doesn't understand how corporations and money actually work. In ''The Corpse on the Canopy'', Pelant drains all the bank accounts containing the $4.6 billion dollars accumulated by the Cantilever Group, leading to its collapse and leaving Hodgins broke. Aside from the fact that it makes no sense that all that money would all be in the same place, ready to be drained by Pelant just like that (this is probably an instance of HollywoodHacking), there's absolutely no reason Hodgins couldn't reverse Pelant's work. It's not like the money was given to Pelant in the form of cold, hard cash; it's just an electronic record that says that the money was taken out of those accounts. All Hodgins would have to do is call his bank and say, "I did not authorize those transactions. Put it back." Actually, the bank would probably look askance at a rich man (also the sole heir to the third largest private corporation in the US), for no reason whatsoever, giving all his wealth to some random investment account, and would seek verification of some kind. Also, an extremely large corporation suddenly going bankrupt just like that would trigger much bigger consequences that just "Oh, Hodgins has to live by his salary now". For example, it's stated that a large chunk of the funding for the Jeffersonian comes from the Group, but no mention of funding issues is ever made.
* CrossesTheLineTwice: Billy Gibbons (Angela's father) forcing Hodgins to get a tattoo of her and then leaving him in the middle of the desert. Good thing he lived. And this is after promising Angela that he won't seek revenge. And then he does it ''again'', this time because Hodgins refuses to let him name the baby something ridiculous.
* EnsembleDarkhorse: Dr. Gordon Gordon Wyatt. An overall polite and nice guy who just happens to be played by Stephen Fry.
* FanonDiscontinuity: Some fans prefer to think the ''Series/SleepyHollow'' crossover didn't happen, or at least is non-canon to the ''Bones'' universe. Not necessarily because it was ''bad'', but because of confusion regarding {{Shared Universe}}s and the clash of tones and styles between the two shows (one being all about science, the other being all about the supernatural). If the two shows do indeed share a universe; the entirety of Brennan's skepticism around the supernatural is thrown out the window, with magic and spirits all being 100% real. In its regular episodes, this show has only [[SkepticismFailure hinted at]] [[MaybeMagicMaybeMundane the supernatural]] occasionally, with things such as Avalon's powers and the ghosts of Booth's dead war buddy and Brennan's mom.
** In the Season 9 premiere, Hodgins mentions he wanted to record ''Sleepy Hollow'', further putting into question the crossover episode's canonicity.
** To be completely fair, the ''Bones'' side of the crossover can stand on its own, follows the show's typical rules for the most part, and has some good moments such as Brennan's prank on Booth. It deserves at least one watch for each viewer to form an opinion.
* FunnyAneurysmMoment: "The Tiger in the Tale" has Bones ponder running for U.S. President and when Booth is mildly skeptical, she quips that "Donald Trump has considered running for President". A few years later, in 2016, Donald Trump is actually ''won'' the election, with his campaign and subsequent win being highly controversial and divisive.
* GratuitousSpecialEffects: A particularly egregious example occurs in at the end of an episode where Bones and Booth start shooting nerf guns at each other. The balls are clearly CGI and the actors are clearly pumping empty guns, and it rather begs the question why not just use real nerf balls and save the special effects budget?
* HarsherInHindsight:
** The episode where Booth finds his and Brennan's new house, when they're adorably gushing about how perfect it is and talking about how they can have Wendell fix it up and can plant cherry trees--and really many of their sweet home scenes in that house in later episodes--are harsher knowing that, in the Season 9 finale, [[spoiler: three armed Delta Force agents attack Booth to silence him, and in the ensuing fight, the house gets so many holes blown into it that it comes out looking like Swiss cheese by the end. By Season 10, the family has moved into an entirely different home]].
** [[spoiler: "The Bones on the Blue Line" had Sweets suffer PTSD from someone dying right in front of him, being faced with his own mortality. About five seasons later, he's killed in the season 10 premiere.]] Really, ''anything'' involving [[spoiler: Sweets]] could count as this now, from his relationship with [[spoiler: Daisy]], to Bones and Booth insulting him, and treating him like he's worthless, etc.
** Like the above example, pretty much anything with [[spoiler: Max]] is harder to watch now that he's gone. In particular, there is one episode where Brennan [[spoiler:pretty much kicks Max out of the family for not picking up her calls because he lost his phone while taking care of baby Christine]].
* HilariousInHindsight:
** "The Man in the Fallout Shelter" is much funnier now that Bethesda owns ''{{VideoGame/Fallout}}''.
** "The Cinderella in the Cardboard" basically predicted Tinder.
** Brennan is very against the idea of anything not scientific, whether it be supernatural, magic, religion, etc. ...And then they did a {{Crossover}} with ''Series/SleepyHollow'', in which the team meets a man born 200 years ago who is partnered up with a modern-day police officer. To top it all of, [[spoiler: Brennan shows a document that no one at the Jeffersonian absolutely can explain scientifically.]]
* HollywoodHomely: The Wiccans in "The Witch in the Wardrobe". Booth is repelled at seeing them naked during their ceremony but when we see them clearly in the light of day all of them are at least slightly above-average lookswise.
* HoYay:
** Many moments between Zack and Hodgins.
** Zack and Vincent seem a bit like a bickering couple in Booth's coma dream.
** Sweets and Vincent share a very, ehem, interesting glance at the end of "The Babe in the Bar".
* HolyShitQuotient: The Season 9 finale ''The Recluse in the Recliner'' has Booth face off against three highly-trained Delta Force agents after being brought down by a blackmailed congressman. Booth nearly dies from his injuries, the house he and Bones shared is [[TrashTheSet left in pieces]], and the episode [[{{Cliffhanger}} ends on the note]] that Booth has been accused of "murdering" the agents.
* IdiotPlot: Pretty much the entire Pelant arc requires the team to be complete morons in order to work. For one thing, the team discover that Pelant can hack anything with a net connection, so what do they do? They leave the cameras, Angela's computer, and everything else the way it is. Then they leave their bank accounts untouched so Pelant can steal all their money instead of withdrawing everything they have and closing their accounts. This is just the tip of the iceberg as to the idiotic things the team has to do to keep this villain from being shot dead within 2 episodes. Worse, if the team had taken these precautions another unrelated plot arc around the same time involving Cam's identity theft couldn't have come to pass.
* InternetBackdraft:
** The Season 8 finale ignited a firestorm of rage over its DownerEnding aimed right at Brennan and Booth's relationship for the sole purpose of generating melodrama and making Pelant into a InvincibleVillain.
* LikeYouWouldReallyDoIt:
** The beginning of the Season 11 premiere (along with the promos for it) try to make the viewers think Booth's been murdered and the team's examining his remains. This isn't really effective, since a show like this wouldn't kill one of its two main characters eleven seasons in, not to mention that within 10 minutes, Brennan determines the remains are not Booth's.
** Similarly, the promo for the Season 8 finale makes it seem like Pelant managed to shoot Booth.
* MagnificentBastard: Max.
* MoralEventHorizon:
** Epps' various murders and sick games are bad enough, but you really see how twisted and evil he is in "The Man in the Cell"" when he [[spoiler: burns a fireman alive, saws his wife's head off while she's ALIVE, sends her heart to Angela, and booby-traps the decapitated head of his wife with a glass capsule containing a highly poisonous powder, which almost killed Cam.]]
** Killing innocent people just because they're in the way was this for Broadsky. Killing criminals and crooks made him vaguely sympathetic, in a Max Keenan sort of way, but this seemed to cross the line. Of course, Caroline has a different opinion:
-->'''Caroline:''' Man sneaks into [Booth's] house, threatens [Booth] with a gun. That's unforgivable. He should be lethally injected just for that.
** Sweets allowing Brennan to think Booth is dead for 2 weeks for reasons that basically amount to ForScience is considered to be an unforgivable act by much of the fanbase, to the point of turning Sweets into TheScrappy for many.
* {{Narm}}: The birth of [[spoiler:Booth and Brennan's baby]]. Slow-motion in a ''manger''.
** The writers kind of realized this and joked during the Paley Center interview that they thought about giving Hart Hanson, his wife, and son a walk-on part at the end of the birth scene as the "Wisemann" family.
** "I don't know what that means." Bones having {{No Social Skills}} is one thing, but her using that same exact phrase ''every single time'' someone makes a pop culture reference got old extremely fast.
** [[BilingualBonus Knowing Norwegian]] and listening to the prologue dialogue of "[[Recap/BonesS4E21MayhemOnACross Mayhem on a Cross]]" will have you laugh as it's so gramatically wrong. And "Absolutt", despite being more or less same word as "abosolutely" is it not used in the same situations as English works differently. Also with Deschanel's hillariously wrong pronuciation of "skalle"(skull) which sounds more Swedish than Norwegian and her correcting the others who actually say it ''[[SurprisinglyGoodForeignLanguage right]]'', and with the police acting nothing like Norwegian police is the cherry on top, which makes it an episode hard to seriously. One can actually see the Norwegian actor wanting to say it's wrong, but not daring to.
* NarrowedItDownToTheGuyIRecognize: Notably averted at least once. [[spoiler:When Creator/WayneKnight (who played Newman on ''{{Series/Seinfeld}}'') shows up, you expect him to be the killer. He wasn't.]]
** [[spoiler:When Creator/RobertEnglund shows up as a high school janitor who had a thing for knives and death you figured he was the killer. Nope! Nice guy all along.]]
** Played very straight with [[spoiler: French Stewart playing a bit role as a fundamental preacher]] who gets shooed away by the cops in the beginning of the episode. He wasn't even in the running until TheReveal (by the characters, at least).
** No, [[http://mckaylaisnotimpressed.tumblr.com/ "Unimpressed" McKayla Maroney]] did not kill a rival gymnast.
* NauseaFuel: The entire concept of the show is about bodies that are mangled too far for regular forensic teams to analyze, so this can be considered par for nearly every episode. Most of the show's openings also involve somebody coming across a dead body that's decomposing and covered in insects, often finding it in the most disgusting way possible.
** The "pony play" episode.
*** Now HilariousInHindsight. This troper rewatched that episode recently and thought of something [[WesternAnimation/MyLittlePonyFriendshipIsMagic completely different]].
** "The Princess and the Pear". Guess what [[http://en.wikipedia.org/wiki/Pear_of_Anguish the "pear"]] is. And a version is made for [[NightmareFuel use further south]]. If it's any comfort to folks, Pears of Anguish don't actually work -- they're psychological torture as the force needed to use them on either location is more than a Pear could exert. The Pear would break long before the human would.
** "The Critic in the Cabernet". Red wine. Body. How do you think they discover it? ...EWWWW! The liquefied man was somewhere between this and NightmareFuel.
** Then there's the flattened girl who is often being compared to a pizza. They even use a piece of sheet metal to pry her off the cardboard she's stuck to. [[SarcasmMode Thanks a lot.]]
** Then there's the person that was in used fry batter stuff... it's [[NauseaFuel the usual]], right? Bones says that it's not her department and walks off... and then, when they pull the body out, the skin starts falling off, the organs start slipping out, and Bones quickly returns, since it is now in her department.
** "The Babe in the Bar": an episode with a person who drowned in the mold of a giant chocolate bar. All of the decomposition gasses were trapped in her body and liquified it. Also, they didn't find the body until [[NauseaFuel after the bar was set and they had begun cutting it]]. Cue liquidy goo spewing out of the giant candy. Imagine if they had started eating it before they found her?
** "The Bullet in the Brain": Aside from [[spoiler:the Gravedigger's head exploding and seeing her headless body]], there's also [[spoiler:the woman's body half-dissolved in lye, that Brennan and Booth find. Both of them immediately start retching. Keep in mind that they have been working together for about five years by this point, and Brennan has identified remains from mass genocide graves.]]
* NeverLiveItDown
** Bones shooting an unarmed man. [[RunningGag He was trying to set her on fire.]]
** Booth shot an ice cream truck's clown head that was playing the music too loudly while he was on the phone. Even Brennan was predicting it as soon as it happened.
* OnlyTheAuthorCanSaveThemNow: A villain example: [[spoiler: Pelant surviving BoomHeadshot. Booth's bullet manages to miss his brain stem and all other vital bits, going out through his right cheek. The worst injury he suffers from this is a discolored and blinded (but otherwise intact) right eye and maybe some missing teeth, the rest being just scarring from where he stitched his face back together. It's clear the writers saved him for the sole purpose of dangling him over the team's heads for yet another season. They finally offed him early in Season 9, so it's likely he just lived to give them a reason to hold off the wedding.]]
* ParanoiaFuel: Pelant's [[HollywoodHacking computer voodoo]] is this in-universe. Imagine a sociopath who has complete control of any electronics and can track you no matter where you go unless you go completely off-grid, and even then he might try to hack a satellite or your car's GPS. If you get on his short list, he WILL find you, and God only knows what your fate will be. Granted, out-of-universe it becomes severe {{Narm}} to most viewers, but Pelant's mere presence in DC at the start of season 8 caused Hodgins to force everyone to forgo any form of computer electronics for the entire investigation, due to the fear of Pelant hacking them again and sabotaging the entire operation.
* PortmanteauCoupleName:
** Hodgela, for Hodgins and Angela.
** Booth and Brennan are usually abbreviated to BB, but the introduction of [[spoiler:Booth's girlfriend in season six, whose surname also starts with a B]] has led to a few fans crying for Teeley.
** Also, Swaisy for Sweets and Daisy.
* PrimalFear:
** [[BuriedAlive The Gravedigger]].
** Many victims' deaths qualify as this.
*** There was one episode where they realized the victim had been stabbed in the neck. That didn't kill them. It just mostly paralyzed them so that when they were buried alive in concrete, they tried to swim to the surface with only their little finger.
*** The SERBERUS soldier Pelant killed. Bones and Cam come to the conclusion that Pelant tortured him by continuously stabbing him in the spine with needles until the extreme pain put too much stress in his heart, killing him.
* ReplacementScrappy: James Aubrey, the FBI agent who joins the team after [[spoiler: Sweets' death]]. Initially, at least. He managed to win a large portion of the fandom over during the course of the season (though certainly not everyone). As of the Season 10 finale, he's probably more of a BaseBreakingCharacter.
* RescuedFromTheScrappyHeap:
** When Cam first joined the cast in Season 2 to replace Dr. Goodman, fan reactions to her were mixed at best. Many fans bemoaned the fact that Dr. Goodman left right after spending his character arc in Season 1 bonding with and growing closer to the rest of the team, and hated the fact that Cam was so much harsher and more strict towards Brennan than Goodman was. The fact that Cam and Booth briefly rekindled their old romance (standing in the way of the FanPreferredCouple) did not help. However, once Brennan and Cam became friends, the fans warmed up to her along with Brennan. Cam and Booth broke up right afterwards (but have remained good friends ever since), which finally seemed to satisfy any last animosity fans had for her.
** Repeated interference in the lives of his patients for his own agenda which amounted to malpractice, but which somehow inspired the other characters to rave about his professional chops, made Sweets a BaseBreakingCharacter for years, but eventually fans got to loving him, as evidenced by [[spoiler:general outrage and sadness when he died in the Season 10 premiere]].
** James Aubrey was almost universally disliked when he initially joined the cast as [[spoiler:Sweets's [[ConvenientReplacementCharacter replacement]] after his death]] in Season 10, though several fans [[RescuedFromTheScrappyHeap warmed up to him over the course of Season 10]], [[BaseBreakingCharacter but certainly not everyone]]. The episode immediately after the two-part premiere deals with how Booth doesn't think much of Aubrey initially.
* SeasonalRot: While ''Bones'' arguably never got truly pronounced seasonal rot and managed to maintain relatively consistent quality and preserve most of its integrity to the very end, many fans will acknowledge some slumps in the show's history:
** {{Flanderization}} took Bones from being somewhat a socially inept and awkward, yet intelligent and strong woman, to being basically a clueless android who has no idea on how modern society works.[[note]]The final season episode "The Brain in the Bot" is a commentary of sorts on this: Brennan meets an intelligent robot that speaks pretty similar to her.[[/note]] It doesn't help that which characterization's used is DependingOnTheWriter.
** Thanks to the 2007 Writers' Strike, the end of Season 3 suddenly [[spoiler: made Zack the Gormogon's apprentice without any warning whatsoever]].
** For some people, the beginning of Season 7 is this for skipping past the Bones/Booth RelationshipUpgrade. After years of WillTheyOrWontThey, they become a couple off-screen during the TimeSkip, because... [[BabiesMakeEverythingBetter baby]].
** While [[BrokenBase not everyone will agree]], the [[InvincibleVillain Pelant]] [[ArcVillain arc]] could count as this.
* TheScrappy:
** During her run as Booth's girlfriend (and thus, serving as an obstacle for the FanPreferredCouple) in Season 6, Hannah Burley became Public Enemy #1 in the eyes of the fandom. The scene that really cemented the audience's hatred of her was when she was in the hospital after being shot; when Brennan visited her, Hannah more or less demanded Brennan's sunglasses as a Get Well present, which fans found to be incredibly rude and inappropriate. To this day, she is still almost certainly the most hated character to ever appear on the show.
** Avalon. Every time she shows up in an episode, the show (which normally espouses basing everything on cold hard science and facts and mocks the very concept of a profession like hers) suddenly starts treating it like there might actually be something to her powers, while the writers make up situations so she turns out to be right a ridiculous amount of the time and everybody who dares not believe her is either called out by her or Angela, or turns into a believer.
* ShockingSwerve:
** The third season finale, with the revelation that [[spoiler: Zack Addy, the team's awkward lab rat, had assisted a serial cannibal, with no warning whatsoever]]. According to the actor, the twist was basically decided at the last minute.
** Also, the tenth season premiere, [[spoiler: with Sweets' death. While characters have died on the show before, Sweets had been a major character for 6-7 seasons, and had plotlines second only to Booth and Brennan, not to mention being killed off in a season premiere.]] Plus, the twist had been kept completely under wraps until the episode actually aired.
* {{Squick}}: [[spoiler: Booth's [[BoomHeadshot handiwork on Pelant's face]] hits the trifecta of {{Squick}}, BodyHorror, and EyeScream: the right side of his face got completely blown open from the inside, and the right eye looks like some sort of cheap glass eye, completely blind and useless. Pelant had to triangle-stitch the wound without any anesthetic, and even after healing, the scars are still VERY visible. It would've been nice if Booth had killed him with that shot, but seeing Pelant's PlotArmor finally crack was still impressive.]]
* StrawmanHasAPoint: In "The Brain in the Bot", an anti-robot activist tells Aubrey that people who claim to be a positive force in the world like the VictimOfTheWeek are actually only in it for the money, and says that the episode's victim was likely selling his A.I. meant to help autistic children to make robotic weapons instead. Later on, Booth and Aubrey find out that the victim ''was'' selling his A.I., though only to make "living sex dolls", not weapons. Turns out the guy wasn't so wrong on his former point...
* TheyWastedAPerfectlyGoodPlot:
** The writers initially seemed to be gearing up for another big ArcVillain with the Ghost Killer, with there being no consistent MO for the killings (unlike Broadsky or the Gravedigger), barely any clues on who the murderer could be (unlike Pelant, with whom the bigger problem was actually ''catching'' him), and no one but Brennan believing the serial killer even ''existed''. Then, in ''The Nail in the Coffin'', the writers instead took the route of TheKillerBecomesTheKilled, and used the Ghost Killer arc as a "bridge" to jump into the government conspiracy plotline that took up the S9 finale and the beginning of S10.
** The plot of Hodgin's mentally ill brother, Jeffrey. It puts a heavy emotional and financial strain on Hodgins, specially in a moment where all their money was stolen by Pelant. The brother has an extreme psychological issue that makes him unable to live in society and their parents threw the boy in a institution, hiding his existence of Hodgins, but said brother is never brought up again after the episode he is introduced.
* UnintentionallyUnsympathetic: For some viewers, Brennan's extreme literal-mindedness, [[InsufferableGenius I'm always right attitude]], and lack of empathy and imagination gets old fast.
** Brennan’s abandonment issues with her father. This is brought up multiple times with her continuously forgiving her father only for her to be suspicious of him again the next time she sees him. While this in itself is annoying, what really makes Brennan this is that she is forced to do the same thing to Booth in the S7 finale. Not only does she not see anything wrong with her actions, she doesn’t notice how hurt Booth was at losing three months with his daughter but her as well. Yet despite this, she still has the same abandonment issues with her father.
** Also, her attitude at everyone's skepticism of the existence of The Ghost Killer. She acts as if everyone's in the wrong for not immediately going along with her belief/obsession that the serial killer is real, while ignoring there's zero evidence backing her up, when typically ''she'' doesn't believe in anything that has no evidence behind it. Also, as Booth points out, since ''Pelant'' was the one who brought up the Ghost Killer in the first place, it could've easily just been a ploy of his to make Brennan believe keeping him alive was necessary. Clark actually manages to [[TakeThat call her out]] of this behavior at least twice:
--->'''Brennan:''' So you don't believe me either.
--->'''Clark:''' It's not about belief. It's about the evidence. ''You'' taught me that.

--->'''Brennan:''' This evidence should've been linked to the Ghost Killer immediately.
--->'''Clark:''' I did. I also noted the other fingers. Unless you're too arrogant to look at my findings.
* WhatAnIdiot: Angela getting herself arrested for refusing to testify at Max's trial. Yes, she was "protecting" [[HeterosexualLifePartners her friendship]] with Brennan, but it's the team's job to testify what they know whether they like it or not, and she's got her BFF's permission to testify anyways. Not to mention that her testimony (identification of the body) would've caused relatively small damage to the defense (unlike Zack's or Booth's, who testified about the murder weapon and opportunity, respectively), so ultimately she got herself locked up over barely anything.
* TheWoobie:
** Sweets and, to a lesser extent, Zack. And if you don't feel bad for Hodgins during season 4, there's something wrong with you. Heck, Brennan herself-underneath that InsufferableGenius exterior lies a very vulnerable, fragile soul-the times when it's exposed tend to [[TearJerker quite sad.]]
** Wendell as of Season 9. [[spoiler: He was diagnosed with a specific strain of cancer with an extremely high mortality rate. His father died of lung cancer and wasted away the little years he had, so Wendell was not hopeful for his already minuscule chances. On top of that, to relieve the pain from his treatments, he must take medicinal marijuana. But this means that he cannot work at the Jeffersonian after Cam found out. All of this came down on a guy who was perpetually happy and all-around good-guy. Even Bones lament how it seemed like he was being unjustly punished.]]
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