* AccidentalInnuendo:
** Traps Illustrated, if you know [[UnsettlingGenderReveal what the word trap can also mean]].
** From episode 11: "Nothing says I love you like 200 ft. of parachute cord and a cargo net!" Looks like Freddy is also into bondage.
** In the first few episodes of Season 2 Daphne goes on and on about how she found a "real man," one who isn't obsessed with traps over her.
* AlternativeCharacterInterpretation:
** Mayor Jones: [[spoiler: did years of BecomingTheMask leave him with some affection for his "adopted" son? Did he save Fred's life because he cared, or because he feared the wrath of Brad and Judy Chiles?]] [[spoiler:"Nightmare in Red" confirms that he truly did grow to love his son. He didn't show it usually because his good side was literally trapped in his subconscious. Through talking to said good side, Fred forgives him and acknowledges him as his the only true father he ever had.]]
** Fred's almost narrow-minded obsession with traps and difficulty reading other people have led a few viewers to conclude he falls somewhere on the Autism spectrum.
** Velma: Did she really [[AllLoveIsUnrequited love Shaggy]] or [[PairingTheSpares was he just the other guy to her]], knowing that Daphne really liked Fred?
* AngstWhatAngst: The ending. [[spoiler:A CosmicRetcon results in a universe where just about everyone is happy and has a perfect life. However, besides being initially confused by the changes and expressing surprise at the new developments, none of the gang seem to have problems adjusting to the universe. Namely Fred, whose parents ''tried to kill him'' and now are {{Doting Parent}}s despite having been raised by the man who is now his principal; as well as Daphne, who doesnít seem to feel bad that her sisters are put down and donít have successful careers in this universe. On the other hand, since this scene was towards the end of the finale, there understandably wasnít enough time to bring up the issues and itís possible that RippleEffectProofMemory will eventually let the gang remember both timelines to make adjusting to this timeline easier.]]
* AuthorsSavingThrow: "Dance of the Undead" switched the Hex Girls back to their original outfits ([[FandomNod with a tongue-in-cheek reference to the complaints about them]]), and featured them prominently assisting Shaggy and Scooby in defeating the Ska Zombies.
* BadassDecay: Mr. E's actions never quite stop being threatening or competent, (with the exception of one instance of being OutGambitted) but you have to admit knowing he's [[spoiler:grotesquely overweight and [[LeftTheBackgroundMusicOn actually playing his background keytar music]]]] doesn't do a whole lot for his air of menace, and it gets particularly bad when [[spoiler: he ends up being personally intimidated by a confrontational ''Shaggy'' at one point.]]
* BaseBreakingCharacter:
** Scooby and Velma. Some sympathize more with Scooby than Velma in the "love triangle" with Shaggy, while some sympathize more with Velma. And some sympathize with neither of them because they both displayed creepy {{Yandere}} behaviour towards Shaggy. Many longtime Velma fans are twisted oved her persona in the cartoon as well. There's a split who prefer her snappier portrayal while other fans think it ruins her.
** The new look of the Hex Girls is very divisive, as well. A future episode has them back in their original outfits, however [[FandomNod along with a line stating that there were people who liked their old looks.]]
* BrokenBase: There are a few fans that aren't really pleased with [[spoiler:the CosmicRetcon ResetButton StealthPrequel ending]].
* CargoShip: Fred and traps. Seriously, he can't walk past a net or a cage without swooning over it.
* CompleteMonster: The GreaterScopeVillain, the [[EldritchAbomination Nibiru Entity]], is a member of a normally benevolent inter-dimensional alien race called the Anunnaki; his own kind considers him the most evil member of their entire species. He's spent untold centuries corrupting and manipulating the people around him, especially the {{Team Pet}}s of mystery solving teams, by perverting his species' ability to use animals as mediums to communicate, all working towards [[SealedEvilInACan freeing him from his prison]]. In the process he's ruined and ended countless lives through his {{Unwitting Pawn}}s (including [[BigBad Professor Pericles]], who the Entity turned into a murderous psychopath) without a second thought. When he's finally released in the SeriesFinale, he proceeds to [[YouHaveOutlivedYourUsefulness gleefully eat his loyal minions alive]] along with Mr. E. He follows this by turning Crystal Cove into HellOnEarth and devouring the ''entire'' town with sadistic glee, planning to move on to the rest of the universe when he's done, all for the sake of power. When Mystery Inc. finally kill him, erasing him from time in the process, we see what Crystal Cove would've been like without his influence: a normal town with everyone living good, happy lives, showing just how much pain and misery he was truly responsible for.
* ContinuityLockout: As the show progresses and all the plot points and backstory are piled on about the questions about the Conquistadors and the original Mystery Incorporated, it becomes rather unfriendly to newer viewers regardless of the PreviouslyOn segments. The show's ending, however, at 52 episodes and 2 seasons, may mitigate this. It is nonetheless a lot better in [[BetterOnDVD one sitting]].
* CounterpartComparison: [[HilariousInHindsight Hilariously enough]], there have been comparisons to ''Mystery Incorporated'' with ''WesternAnimation/GravityFalls''.
** Both shows have a strong emphasis on ComedicSociopathy, family and friendship, dramedy, and supernatural mysteries, along with a MythArc involving a reopened case about a missing predecessor(s) who is connected to an important object found by TheSmartGuy in the first episode.
** Both shows were two seasons long with a third season considered, as well as having infamously long hiatuses.
** Both feature Creator/LindaCardellini as a prominent major character, involved in a crush with TheSmartGuy, and plays a major role in the series finale. (Wendy/Hot Dog Water)
** Both feature a [[ComedicSociopathy comedic sociopath]] relative wearing a SuitWithVestedInterests and glasses, takes the tourism business seriously, and is supposedly allied with the protagonists, only for their true motives and true identity to be revealed in a (mid-)season finale, leading to much heartbreak. (Grunkle Stan/Mayor Jones)
*** He becomes wary when TheSmartGuy shows him the important object, as it turns out later that he is involved in the disappearance of that person(s) and knows more than he lets on, though Velma showed it to Mayor Jones in the first episode while Dipper showed it to Stan in the final episode of the first season.
*** At one point, after a rift grows between him and his estranged relative, the main characters end up having a JourneyToTheCenterOfTheMind episode where they find his subconscious, with his relative initially accusing him of starting trouble again only to discover he's trying to help them, then later reconciling with each other after being chased away by the monster-of-the-week and before leaving.
*** A difference is that Stan, while he can be a jerk, does genuinely care for his relatives and sticks up for them more regularly than Jones does.
** Both feature rich/high-class [[AbusiveParents abusive]] and [[ParentalNeglect neglectful]] parents.
** Both take place in tourist towns full of ApatheticCitizens and with a tourist-bait name.
** There's an ElectionDayEpisode between two SuitWithVestedInterests characters, with the one allied with our protagonists winning, though it doesn't last because it turns out he's a criminal, resulting in him being replaced by someone who is slightly more competent but is unambiguously good.
** There's a Valentine's Day episode featuring a supposed god (Love God is genuinely Cupid but [[TheyLookJustLikeEveryoneElse he looks like a regular guy]], Aphrodite looks like a monster and is actually a costume) casting love spells on people.
** The first season prominently features a character in a SuitWithVestedInterests that is AmbiguouslyEvil and is a VillainWithGoodPublicity that only the protagonists aren't fond of, only for their true motives and status as the ArcVillain to be revealed at the end of the season, which turns everyone against him (namely the police) and gets him thrown in jail, but still has an influence on the show's events. He ends up getting redeemed by the end of the show. (Gideon/Mayor Jones)
** The local police department is led by a [[PoliceAreUseless dunderhead]] ManChild sheriff(s) that initially hates the protagonists (and has arrested them on a number of occasions) and enforces said VillainWithGoodPublicity for the first season, but ends up [[FireForgedFriends becoming good allies with the protagonists]] after the reveal that said villain is actually evil. The sheriff(s) also turns out to be AmbiguouslyGay (or bisexual) and/or is happily married/openly in a romantic relationship.
** A one-eyed entity is the BigBad of the show.
** An EldritchAbomination is the ''true'' BigBad of the show and wrecks the town to the point that the townspeople are screwed (''Gravity Falls'' had everyone either captured or in hiding, while ''Mystery Incorporated'' had [[KillEmAll killed them all]]), but things revert to normal/better conditions with no one remembering the events or [[LetUsNeverSpeakOfThisAgain not wanting to speak about it again]].
** The show ends with an EarnYourHappyEnding, with the cast achieving a happy life, finding closure with each other, and leaving town.
* CrazyAwesome: Just about all of the Monsters of the Week qualify to some degree, but Ernesto, Mary Ann Gleardon, Alice May, and Mrs. Wyatt really stand out.
* CreepyAwesome: Professor Pericles. Creepy? Oh yeah. Awesome? Creator/UdoKier makes it so.
* CriticalResearchFailure: In the first episode, Angel Dynamite gives the call letters and frequency of her radio station, naming 101.4 on the AM dial. Two problems with this for anyone who has ever taken a look at a radio: AM stations are between 540 and 1610, in increments of 10 and no decimals (e.g. 760 AM, 1370 AM). In the US, FM stations, which do have decimals, only use odd numbers for the tenths place (e.g. 101.1, 101.3, 101.5 but never 101.4). Alternatively, this could be FiveFiveFive applied to radio stations.
* EarWorm:
** [[http://www.youtube.com/watch?v=KWvYN4ftNHs&fmt=18 Trap. Of. Love.]]
** In "Dance of the Undead", there's the BattleOfTheBands [[https://www.youtube.com/watch?v=GzW5ApHYglU between the Ska Zombies and the Hex Girls]].
** The "Dance in my Pants" song in episode 7 "In Fear of the Phantom".
** "Yer Dead Right Mates" and "We're The Good Bad Girls" from episode 44 "Dance of the Undead".
* EnsembleDarkhorse:
** Marcy "Hot Dog Water" Fleach due to being [[spoiler:the gang's SixthRanger]] and especially all of her LesYay with Velma.
** Alice May, mainly for the reason stated below.
** Not to mention, Creator/HarlanEllison for fairly obvious reasons.
* EvilIsCool: Professor Pericles, the chief BigBad, is easily the most popular and memorable villain in the show for this reason.
* EvilIsSexy:
** Alice May, [[spoiler: especially as Obliteratix in episode 25.]]
** For some people, Mayor Jones, apparently.
* FanNickname: As it turns out, [[spoiler:Nibiru is not the name of the thing inside the sarcophagus seen with the cursed treasure. Nibiru is the name of a certain time when the thing's homeworld and Earth are able to interact with one another.]]
* FunnyAneurysmMoment:
** A lot of Mayor Jones' "wacky" moments from early in the season become this after seeing the finale...
** "Mystery Solvers Club State Finals" is an amusing episode, and the reveal of [[spoiler:Mudsy]] as the villain is rather funny. Season 2 then starts to imply [[spoiler:that the animal or any unique companion to a Mystery solving group will turn evil because of the mystery of Nibiru]].
* GeniusBonus:
** Daphne's "radical idealist friend" Ernesto seems to be named after Ernesto "Che" Guevara.
** "Hatecraft"'s ravenous follower Robert E. Howard is named after the author of the Franchise/ConanTheBarbarian novels, who really was a correspondent of Lovecraft's while he was in his twenties.
* GrowingTheBeard: The first season, while starting strong, did struggle with balancing the mysteries, story arc, humor, and romance. As the first season progressed and romance mostly dropped, the show caught a better balance, using the characters to play off each other [[CharacterDevelopment and develop]], and focusing on the main StoryArc with [[BreatherEpisode goofy episodes]] in-between.
* HarsherInHindsight:
** Mayor Jones's voice actor, Gary Cole, [[RoleAssociation also voiced]] [[WesternAnimation/BatmanBeyond Infiltration Unit Zeta]]. Zeta's first anti-terrorism mission was to pose as an innocent man associated with terrorists, which required him to be around the man's family. Upon seeing the life in the man's family--particularly, seeing his daughter ride a bike for the first time, he had a HeelFaceTurn, because he couldn't bear to tear apart a family. [[spoiler:Mayor Jones deprived Brad and Judy of their own baby son by kidnapping him as a hostage, and later attempted to turn him into his VillainousLegacy all while being [[ParentalNeglect incredibly neglectful]].]]
* HilariousInHindsight:
** In "The Shrieking Madness", Shaggy reacts unfavorably to the vegan burgers being served. Funny because Casey Kasem insisted that Shaggy become a vegetarian in order to bring him more in line with Kasem's strict vegetarian diet.
** Also in "The Shrieking Madness", Ernesto gets his followers to consider protesting against shawarma, two years before [[Film/TheAvengers2012 a certain superhero blockbuster]] unexpectedly [[TheRedStapler made shawarma a well-known food]].
** Matthew Lillard becoming the new voice of Shaggy despite being threatened by the animated Shaggy and Scooby in ''Film/LooneyTunesBackInAction'' for his performance in the first live action movie.
** The amount of [[CounterpartComparison similarities]] between this and ''WesternAnimation/GravityFalls'' have become this. One of the major points is that Mayor Jones keeps complaining about how Crystal Cove's tourism sucks because their monsters aren't real and the Mystery Inc. keeps debunking them as hoaxes, but as Gravity Falls' tourism shows, [[CaptainOblivious people are so inept at telling the difference between hoaxes and true supernatural that they'll pay money to travel there and buy merch anyway]], and since both towns have ApatheticCitizens, Crystal Cove could easily take a cue from Gravity Falls.
* HollywoodHomely: in ''The Creeping Creatures'' the landlady wouldn't let Velma sleep in the same room as Daphne because she (the landlady) thought Velma was a boy. In the second season Velma's HollywoodHomely has became a RunningGag, almost at [[WesternAnimation/FamilyGuy Meg Griffin]]'s levels.
* JerkassWoobie:
** Velma. You can't help but feel sorry for her when [[spoiler: Shaggy picks Scooby over her. Granted, Shaggy probably wasn't a good match for her anyway...]] [[spoiler:Feel more sorry for her; she's all alone now that the gang's split up. Oh and remember...''she's being blamed for it by Daphne''.]]
** Sheriff Stone can fall into this territory too, especially in "Dead Justice" and "All Fear the Freak".
** Danny Darrow [[spoiler: when he was a child; he and his family go crazy with greed after finding a piece of the planespheric disc, and their house sinks underground where he's forced to live out his life (about 75 years), obsessed over the piece, while he and his family grow old, and they all die.]] A run in with the original mystery inc. leads him to set traps all over the house, and he almost kills the current ones with them, and later with a fire poker. In one scene, the gang sets a trap, and Scooby lures him in while pretending to be his mother, he responds with a genuine hopeful smile and says "Mommy, you came back to me?" [[spoiler: Despite knowing that she died years ago.]]
** [[spoiler: The members of the original Mystery Inc., with the possible exception of Professor Pericles, due to how the curse of Crystal Cove completely ruined their lives and warped them all into awful people, with both Ricky Owens and Cassidy Williams undergoing a doomed romance and ending in RedemptionEqualsDeath, while Brad Chiles and Judy Reeves start as decent people who love each other and their son but gradually turn into hateful psychopaths who only care about themselves.]]
* MagnificentBastard: Professor Pericles definitely qualifies -- nearly every episode he shows up in, he gets ''exactly'' what he wants, usually at the expense of the gang. "The Wrath of Krampus" was the first time he's suffered a defeat. And that was because the entire town and Rouge Gallery were in on the BatmanGambit.
* MoralEventHorizon: The Nibiru Entity gets one when, after it is freed, it [[spoiler: proceeds to kill Professor Pericles from the inside, EAT Brad and Judy (AFTER they had pledged their servitude), then Mr. E., then the rest of the town, all for power (and you can tell it's enjoying it), and it claims it will go on to devour entire GALAXIES! Then again, it is the most evil Annunaki EVER]]. It's being the cause of corruption of ''all villains'', even Professor Pericles, stands out too.
* {{Narm}} / NarmCharm: Scooby ending his promise to [[spoiler: get the gang back together and go after Pericles with "or my name isn't Scooby Dooby Doo!" either undercuts the tension entirely or just sort of works depending on who you are.]]
* NightmareRetardant: The [[spoiler: Nibiru entity]] is terrifying for the most part, its initial appearance is.....not. Thankfully it doesn't stay in that form for very long, and its new look is a complete 180 in frightening.
* RescuedFromTheScrappyHeap:
** This series has done this for Fred. He used to be the TropeNamer for StandardizedLeader (aka 1-Dimensional Leader). This show's interpretation of the character is arguably the most popular incarnation of the character yet.
** Mayor Fred Jones Sr. was rescued twice. People hated him for being a {{Jerkass}} who put money ahead of his child's safety. The first time he was rescued [[spoiler: he was revealed to be the Freak of Crystal Cove, the first season's BigBad, meaning that one was ''supposed'' to dislike him, and he fell into LoveToHate as a truly nasty KnightOfCerebus, or if not then HateSink]]. He was rescued again when it was revealed that [[spoiler: for all his faults, he's actually a better fit for a parent for Fred than his biological ones; Brad and Judy, whose greed exceeded the mayor's due to them being more closely connected to the curse. His best part's reconciliation with Fred and his later {{Cosmic Retcon}}ned self pulls him from being hated.]]
* RomanticPlotTumor: A general consensus for the first half of Season 1 was that too much time was spent on the relationship drama between the characters. It's considered to have gotten much better from Season 1's second half and onward.
* SignatureScene: The "Trap of Love" concert. Overlaps with BestKnownForTheFanservice.
* SurprisinglyImprovedSequel: Considering all the Franchise/ScoobyDoo stuff that was coming out after ''WesternAnimation/WhatsNewScoobyDoo'' ended.
* TheyChangedItNowItSucks:
** While the show is considered very good by a lot of people, a very large amount of old school ''Scooby Doo'' fans ''hate'' it because of things like drastically changing or "derailing" old characters, ditching "Coolsville", focusing more on relationships than mysteries, and not having Scooby Snax (or at least not as prominently). The most passionate of haters even play the "ruin my childhood" card!
** In a more specific example, the Hex Girls were hit with this considerably. While people love that Luna got her original skin-tone back and consider "Trap Of Love" one of the best parts of the cartoon, everything else is divisive. Their new designs received mixed reactions to the point where they later showed up in their traditional looks. Their music style was changed to a more contemporary style which made a lot of fans of their original songs disappointed at the newer versions of their songs, especially "Earth, Wind, Fire, and Air".
* UnintentionallySympathetic: Daphne's sisters [[spoiler:losing their successful careers and marriages in the new timeline]]. It's supposed to be something of a BreakTheHaughty moment where those who succeeded at Daphne's expense were punished while she was rewarded, and Daphne's status as TheUnfavorite is removed. Except, they didn't succeed at Daphne's expense, and her parents, who escape punishment, were the one's who held her in such little regard, and constantly reminded her of it. To make matters worse is that of her sisters, only Daisy was a {{Jerkass}}, three of them didn't show much personality (one of whom went unnamed), and her other sister, Delilah, was ''nicer'' to her than her own parents.
* TheUntwist:
** "The Creeping Creatures" involves a case with three gator-men trying to scare people away from their town. There are only three people around, all of them act super creepy, and just in case that wasn't enough, the shapes of their heads match the three gator-men. Are we even supposed to see a mystery in this?
** "The Secret Serum" tries to fool the viewer into thinking Daphne's mother is the vampire attacking the town. The misdirection might have been more successful if she wasn't accompanied by a very obviously creepy, shifty-looking and pale assistant who's accompanied by creeping sound effects and walks without seemingly moving her feet.
** In "Menace of the Manticore" it was painfully obvious that [[spoiler:Hot Dog Water]] was the Manticore. And since they bring it up in season 2 it could also be a LateArrivalSpoiler.
** The entire point of "The Gathering Gloom"'s mystery. [[spoiler:The rest of the gang chides Velma for immediately suspecting [[ObviouslyEvil Count Evallo]] as the Monster of the Week, and begin investigating the incredibly friendly {{Oktoberfest}}er blonde and her three beautiful daughters. Velma manages to find the evidence to prove Evallo's guilt, with the help of just Scooby and the Sheriff. To make things worse, while Velma was totally right, the Count, being a count, had diplomatic immunity.]]
** In "The Song of Mystery", [[spoiler: not only is Mary Anne is the only other character besides Luis, she's the only child that isn't affected by the song, ''and'' she's just the right height to be the monster!]]
* WhatAnIdiot:
** ''Anyone'' who tries to scare people away in a town where hauntings are a ''tourist attraction''. That's just asking for paranormal enthusiasts to get too close.
*** Then again, that also means that the local authorities are reluctant to stop you if you dress like a monster.
** Also, "the slime monster" [[PhraseCatcher might have gotten away with it, too,]] if he hadn't ''staged an attack in broad daylight!''
*** The intention might have been to [[spoiler: lead someone to trapped victims who needed medical help]].
** The whole gang ''still'' not having realized the gaping hole in Alice May's DaddysLittleVillain con by the time of her reappearance.
** Season 2, Episode 9: [[spoiler:While leaving fake evidence at Dougal [=McGuines=]' house was a somewhat smart move on Gary's part, leaving his own yearbook with his name in it and trying to frame a person that would give the gang evidence was not]].
** Brad and Judy aren't too bright. [[spoiler: Their whole reasoning behind their FaceHeelTurn is to protect Fred from seeking the treasure and becoming corrupted. And thus the predictable outcome to this plan happens: '''THEY''' become corrupted and end up so obsessed with the treasure that they forget all about the son they were supposed to be protecting and willingly hurt him in order to get to the treasure.]]
** In "The Man in the Mirror", Fred ''knows'' that [[spoiler: his parents are searching for the Planispheric disk. So why, oh why, does he lead them directly to its hiding place at the abandoned factory instead of literally anywhere else?]]
* WhatDoYouMeanItsForKids: This show is surprisingly darker, violent, gorier and ''scarier'' than the previous shows have (threats to ''kill the gang'' have occurred, stuff blows up, people get injured, etc.) yet it was rated TV-Y7-FV! Ironically, its sister show ''WesternAnimation/TheLooneyTunesShow'' was rated TV-PG, yet is much tamer.
* TheWoobie:
** Fred. Fred. and Fred. [[spoiler: Episode 26 revealed that he was taken away from his real parents by the mayor and he's leaving to find them. But deep down you can feel him sob and choke because all this time his real parents have been worried sick about him.]] Fred gets it ''worse'' in the Season 2 premiere. [[spoiler: Daphne's moved on, the plan failed, TheBadGuyWins, oh, and he's been living as a hobo for a while now... someone give him a hug. [[ThrowTheDogABone Then his parents move in, and they're just as good as one could hope!]] [[YankTheDogsChain Until they join Mr. E and Professor Pericles]]. And Fred moves out of his house, instead of kicking ''them'' out.]]
** Don't forget Daphne. [[spoiler: She was waiting to marry Fred but Fred has stated that the engagement is off and that Mystery Inc. is Dead. She's last seen crying that everything has just fell apart.]]
** [[spoiler: Hot Dog Water / Marcie]] in Season 2.
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