* AlternativeCharacterInterpretation:
** 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?
*** For those that support the idea of Velma being attracted to women (such as her ShipTease with Marcie), was her {{jerkass}} behavior towards Shaggy during their relationship a result of her not knowing her sexuality yet and forcing herself into a romantic relationship she didn't actually want? And/or did she learn from her mistakes and that's why her relationship with Marcie went better than with Shaggy?
*** Related: Were the implications that she wanted to go further in her relationship with Shaggy real, or her wanting to prove to herself that she ''was'' attracted to him? Or even trying to feel more secure about her own attractiveness (given all the jokes about her being mistaken for a boy or not being worth pursuing)? A bit of all three?
** Shaggy and Scooby's love for Vincent Van Ghoul's horror movies suggests that they are [[NightmareFetishist Nightmare Fetishists]] who continue to be members of the gang because they derives cheap thrills from being scared out of their wits.
** The exact nature of Scooby and Nova's relationship. Most fans seem to automatically assume it to be romantic, although it's extremely chaste, even taking into account this series' more adult tone. Scooby's fantasy with her in one episode is just the two having a nice picnic on a sunny day. That and the fact that much earlier, Scooby seemed to think that Velma's romantic relationship with his non-romantic HeterosexualLifePartner, Shaggy, was a threat to his "best buddy" relationship adds to it as well.
* AngstAversion: Can bring about this to some, but more notably the show received this from franchise creators Joe Ruby and Ken Spears, [[DisownedAdaptation who despised it for being too dark and cynical]].
* AngstWhatAngst:
** At the end of "The Dragon's Secret", upon learning that [[spoiler:Mai Le]] was [[WasItAllALie just using Shaggy's feelings to get what she wanted]], Shaggy is silenced into sadness... only to be seen smiling and fine a minute afterwards in the EverybodyLaughsEnding. Probably since the [[BreatherEpisode episode]] [[{{Filler}} wasn't supposed to add to the plot]] and the writers didn't want to repeat another break-up arc.
** 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 doesn’t seem to feel bad that her sisters are put down and don’t have successful careers in this universe. On the other hand, since this scene was towards the end of the finale, there understandably wasn’t enough time to bring up the issues and it’s possible that RippleEffectProofMemory will eventually let the gang remember both timelines to make adjusting to this timeline easier.]]
* SugarWiki/AwesomeMusic: Fans have always loved the Hex Girls' songs, and alongside new versions of "I'm A Hex Girl" and "Earth, Wind, Fire, And Air", this show gives us another great hit with "Trap Of Love", sung by Daphne about her relationship with Fred.
* 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 over her persona in the cartoon as well. There's a split who prefer her snappier portrayal while other fans think it ruins her. One argument for this portrayal is that [[FreudianExcuse she's a product]] [[CrapsackWorld of her environment]] and she does undergo CharacterDevelopment, while the other side argues that Velma being unsympathizing is a departure from her usual NiceGirl depictions.
* BigLippedAlligatorMoment:
** "Mystery Solvers Club State Finals" has Principal Quinlan, who seems to exist for the sole sake of DoesThisRemindYouOfAnything TheirFirstTime. A NervousWreck, she makes AmbiguouslyGay comments towards Angel, and that along with her becoming HotterAndSexier when she has an AdrenalineMakeover after [[MakesJustAsMuchSenseInContext giving "CPR" to Speed Buggy]] come off as her [[YouNeedToGetLaid being inexperienced with romance and sex]]. [[AllJustADream This is all undone at the end of the episode]] (and the entire episode was dreamt by Scooby, so he has an interesting imagination) and she's a OneShotCharacter, so this ''never'' comes up again in any way.
** From “The Siren's Song”, the Scrappy-Doo exhibit in the mystery museum. Despite upsetting Fred and Daphne (and Velma, Shaggy, and Scooby, if Fred can be believed about them agreeing not to talk about him) none of Mystery Inc. has ever had a problem with venturing to that part of the museum (with his statue) before, and Daphne, before she's cut off, seems to be trying to say that she's never seen his exhibit in the museum before. And it quickly disappears soon after.
** In "A Haunting In Crystal Cove", Shaggy and Scooby are attacked by an uncooked pizza that has come to life by a ghost. The end of the episode reveals that [[spoiler:Pericles]] was just using the traps Fred set up in the house to make it seem like a ghost was haunting the house, such as using gadgets to levitate objects... but that doesn't explain how the pizza ''became sentient and self-aware''. Could be chalked up to having something to do with [[spoiler:the Entity's influence]], but it's never made clear.
** In "The Midnight Zone", the gang infiltrate an underwater factory producing evil robots. Within it they find a room full of baby robots. The purpose of building baby robots that just sleep and cry is never explained or brought up again. Potentially, it's just meant to imply Frau Abigail Gluck - the creator of the base and robots - had gone truly crazy by the end of her life.
* BrokenBase:
** The amount of CrossesTheLineTwice[=/=]ComedicSociopathy jokes. Some are SugarWiki/{{funny|Moments}}, but are others problematic? And if you do consider these jokes as problematic, are these properly addressed?
** If the DarkerAndEdgier and DenserAndWackier tone of the show is a step forward for ''Scooby-Doo'' or takes the fun out of the lax tone that ''Scooby-Doo'' has always had. For example, is the explanation for why Scooby can talk a hilariously awesome way of addressing it or is it just unnecessarily edgy and pretentious?
* CaptainObviousReveal:
** "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 the shapes of their heads match the three gator-men. Just in case that wasn't enough, this is the '''Scooby-Doo''' franchise we're talking about. Are we even supposed to see a mystery in this?
** "Battle of the Humungonauts" attempts to lead the viewer off track by making it seem like constructor Rusty Nails is BOTH Humungonauts. While it does try to be a case where it leaves the clues in the background? The Minner brothers are depicted on their insurance billboards wearing RED AND GREEN TIES respectively. As if the radio commercials aren't obvious enough.
** "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, due to the clues Velma brings up.[[labelnote:Explanation]]The fact that the suspect would have to be someone who has elite computer skills, and that the Manticore has a distinct smell, which are both things that Hot Dog Water possesses.[[/labelnote]] Since they bring it up in Season 2, it could also be a LateArrivalSpoiler.
** "The Song of Mystery" presents the exchange teacher Luis as the suspect for a monster that is sending children into a hypnosis. The only other character introduced is a little girl named Mary Anne, who is the only child not affected. The monster is also too small to be an adult in disguise. It's very obvious who is behind it.
* CargoShip: Fred and traps. Seriously, he can't walk past a net or a cage without swooning over it.
* CompleteMonster: [[spoiler:The [[GreaterScopeVillain Nibiru Entity]] is a member of a normally benevolent inter-dimensional alien race called the Anunnaki, which consider him the most evil member of their entire species. He's spent untold centuries [[TheChessmaster corrupting and manipulating]] everyone 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 freeing him from his prison. In the process he's ruined and ended countless lives through his pawns, including [[BigBad Professor Pericles]], whom the Entity turned into a murderous psychopath. When he's finally released in the finale, he proceeds to 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]].
* CreepyAwesome: Professor Pericles. Creepy? Oh yeah. Awesome? Creator/UdoKier makes it so.
* CrossesTheLineTwice:
** In the first episode, when Professor Raffalo reveals that he was going to rob a bank:
-->'''Daphne:''' But you have a job as a teacher? Why would you need more money?\\
''[{{Beat}} of Professor Raffalo making a YouHaveGotToBeKiddingMe face]''\\
'''The Gang:''' ''[all talking at the same time]'' Oh yeah, my bad.
** Fred's fondness for traps in previous entries is amped up to an obsession in this show, to the point he loves it as much as he loves Daphne and the rest of the Gang and struggles to get his priorities straight. A couple of times, he's also seen with a Trap Magazine, with the cover showing a scantily-clad woman... alongside some actual traps. He seems embarrassed about owning some issues, but he claims he only reads it for the articles ([[NotDistractedByTheSexy which may be true]]). His parents are ''also'' into traps.
** Shaggy worries about Scooby finding out that he and Velma are a couple. When he ''does'' find out by walking in on them making out in "War of the Humungonauts", Scooby says, [[NotMakingThisUpDisclaimer we kid you not]]:
--->'''Scooby:''' Stop it, Shaggy. I'm not stupid. [[HoYay Are you... cheating on me?!]]
*** Later lampshaded by Mayor Jones:
---->'''Mayor Jones:''' The Rogers' kid picks a dog over a girl! What's he thinking?! [[LeaningOnTheFourthWall This isn’t]] [[{{Dramedy}} some reality show!]]
** Mayor Jones when he drops off Fred to meet his old college fraternity:
--->'''Mayor Jones:''' [[AmazinglyEmbarrassingParents Now, I’ve dreamed of the day that you'd be humiliated by my old fraternity!]] Don't blow this [[ItsAllAboutMe for me]].
* CultClassic: Though it didn't achieve the massive, attentive fandom ''WesternAnimation/GravityFalls'' (a show it is frequently compared to) did, and was assumed to be just another iteration of the omnipresent ''Franchise/ScoobyDoo'' franchise, and frequently overlooked because of this, it has gained recognition for its overarching story elements, darker tone, and more fleshed-out characters.
* DracoInLeatherPants: [[spoiler:Misinterpretations of all of Fred's parents have led to some viewing Mayor Jones as the better of the three solely because of his PapaWolf moment at the end of Season 1, helping out the gang in "Wrath of the Krampus", and tight-on-schedule reconciliation with his good side in "Nightmare In Red", despite the fact that he put Fred in a stage of near-death in the first place (not to mention the many times he ''didn't'' show affection towards Fred), he was responsible for ruining the lives of the original Mystery Incorporated in the first place too (as well as ruining Brad and Judy's never-could-be family by taking their son), Fred's wording in "Wrath of the Krampus" implying that Jones only helped out of {{Revenge}} against Pericles, and Jones's good side being just as innocent as everyone else in the Sitting Room including Brad and Judy themselves. According to WordOfGod, the intent was to make Brad and Judy look [[HateSink so despicable]] that Jones would be sympathetic [[DamnedByFaintPraise by comparison]], though this was only the reasoning for why Fred would even consider giving Jones his forgiveness rather than an erasure of Brad and Judy's own status as once loving parents who succumbed to their worst nature due to being victims of the Entity's curse just as Jones was. WordOfGod also confirmed that had he not had Fred as a positive influence in his life, Jones' downward spiral into greed and selfishness would have been even ''worse'' than Brad and Judy's.]]
* EnsembleDarkhorse:
** Marcie "Hot Dog Water" Fleach due to being [[spoiler:the gang's SixthRanger]] and especially all of her LesYay with Velma. Even detractors have cited her as one of the best parts of the show [[spoiler:and her horrifying demise at the hands of Pericles' Nazi robots made serious waves in the fandom.]]
** Angel Dynamite[[spoiler:/Cassidy Williams]] for her cool personality and being [[spoiler:the TokenGoodTeammate of the original Mystery Inc.]]
** The Hex Girls have been this from their very first appearance, so unsurprisingly their return to the franchise was very well received.
** Alice May, for her looks.
** Not to mention, Creator/HarlanEllison for fairly obvious reasons.
** Sheriff Stone, by virtue of being voiced by Creator/PatrickWarburton.
** Mayor Jones for being a BunnyEarsLawyer who is revealed to be [[spoiler:a ManipulativeBastard.]]
** Mayor Nettles, for being attractive, [[ReasonableAuthorityFigure understanding]], and [[RetiredBadass competent.]]
** Delilah Blake for being a [[CoolBigBro Cool Big Sis]] to Daphne and being voiced by Creator/JenniferHale.
* EpilepticTrees:
** The fate of the original Mystery Incorporated members being that they went into hiding and took up new identities, or are at least somehow related to known characters in some way. A few common theories included Mayor Jones being Brad, Angie Dinkley being Brad's brother, Mayor Jones' lover & Fred's mother being Judy Reeves, Angel and Cassidy being the same person or related, and so on. [[spoiler:Ultimately, [[IKnewIt they were right about Angel and Cassidy being one and the same]], and they were kind of close about Judy being Fred's mother, albeit for the wrong reason (it was believed that the woman in the photo was an older Judy Reeves, though they were right about the resemblance between Fred and young Judy).]]
** Whatever Nova meant in "Nightmare In Red" about [[spoiler:things becoming undone once the Entity is defeated. General consensus was that either there would be a ResetButtonEnding in which all of the relationships built during the show would have to start from scratch or that everyone afflicted by the curse would get their good side back and everyone who died because of the MythArc would come back to life.]] [[spoiler:It ended up being a CosmicRetcon in which [[EarnYourHappyEnding everyone is happy with little to no catches]].]]
* EvilIsCool:
** Professor Pericles, the chief BigBad, is easily the most popular and memorable villain in the show for this reason.
** [[spoiler:[[EldritchAbomination The Nibiru Entity]]]] as well. He is incredibly scary and disturbing, even by the standards of a kids show. The fact that he is voiced by ''Creator/ClancyBrown'' certainly helps.
* FanficFuel: Just what happened to Scrappy that made Mystery Inc. agree to never mention him again?
* FanNickname: [[spoiler:The Nibiru Entity]] is actually referred to as [[spoiler:the Evil Entity]] in the series proper, though the credits for Season 2 Episode 13 and Season 2 Episode 15 refer to it as [[spoiler:Nibiru]].
* {{Fanon}}:
** Velma confiding to Marcie about [[spoiler:the events of the show in the new timeline, due to her status as TheSixthRanger and her final scene showing that she isn't against the idea of alternate worlds]], while also making Velma/Marcie a thing.
** Similarly, in smaller circles, Fred confiding to Jones about the same subject since [[spoiler:he's the only character that says they have a [[HaveWeMet funny feeling about their ties to the gang]]]], albeit he's harder to convince, while also dealing with Fred's possible identity crisis in regards to [[spoiler:the situation about all of his parents in the new universe]].
* GeniusBonus:
** Daphne's "radical idealist friend" Ernesto seems to be named after Ernesto "Che" Guevara.
** Professor 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:
** A lot of Mayor Jones' "wacky" moments from early in Season 1 become this after seeing the season finale...
** Mayor Jones being rumored to have eaten a live bear in his college days. [[spoiler:He gets eaten by the Entity at the end of the show, but it's played for NightmareFuel[=/=]TearJerker.]]
** "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]].
** In "When the Cicadas Cry", Mayor Jones entertains the idea of having Fred getting EatenAlive by the Cicada Monster [[ParentalNeglect for a boost in tourism]]. [[spoiler:At the end of Season 1, he nearly kills him in a confrontation but [[ConscienceMakesYouGoBack can't bring himself]] [[PapaWolf to do it]], and at the end of the show, he himself gets eaten alive by a ''real'' monster.]]
* SugarWiki/HeReallyCanAct: While Creator/FrankWelker has always been seen as an excellent voice actor, this show really gives him the chance to show his acting chops off, with Fred having a much more involved role [[spoiler: especially with his parents' involvement.]] With the Season 1 finale in particular, his [[BrokenPedestal anger and grief]] at [[spoiler: discovering that Mayor Jones isn't his true father and that almost everything he's known has been a lie, to the point that he disbands Mystery Inc.]] comes off as ''chilling''.
* HeartwarmingInHindsight:
** Angel helping the mascots save their friends in "Mystery Solvers Club State Finals", because she herself is the [[spoiler:TokenGoodTeammate of the original Mystery Incorporated who are now all gone and/or bad people, and thus she technically represents her old club in the reunion.]]
** Creator/CaseyKasem PassingTheTorch of being the voice of Shaggy to Creator/MatthewLillard while playing as Shaggy's father became this when his final lines in the show where [[SoProudOfYou telling Shaggy how proud he is of him]] before he would pass away shortly after in real life.
* HilariousInHindsight:
** In “Escape from Mystery Manor”, Angel gives Daphne the diary of Cassidy Williams, and the first thing she reads out loud from it is an entry about how hot Ricky is. [[spoiler:Angel is Cassidy.]]
** Years after this show concluded, a popular meme would be Shaggy being a [[MemeticBadass badass]] (due to ''[[WesternAnimation/ScoobyDooLegendOfThePhantosaur Legend of the Phantosaur]]''), followed up by the meme of his source of power being because he's an EldritchAbomination, is this trope, [[spoiler:since the show reveals that Scooby is ''also'' an EldritchAbomination (or at least a descendant of one).]]
** Shaggy's parents forcing him to join the military became this, since a popular fan-theory was that Shaggy was drafted to fight in the UsefulNotes/VietnamWar.
** When visiting the Spook Museum, Daphne sees a wax statue of Flim-Flam and laments that a 20-years-to-life prison sentence is a bit too harsh for an underage con artist. She then glimpses a figure of Scrappy Doo, prompting Fred to remind her that they all agreed to never speak of him again. This scene became much more amusing with the release of ''WesternAnimation/ScoobyDooAndTheCurseOfThe13thGhost'', which marked the return of Flim-Flam and hit the final nail in Scrappy's coffin by having Velma outright ask "What's a scrappy?" when his name is mentioned.
** The show had some criticism, particularly from the original Scooby creators, about being too dark and cynical for a Scooby franchise entry. Flash forward a decade to the release of ''WesternAnimation/{{Velma}}'', and ''Mystery Incorporated'' looks positively fluffy by comparison, according to some viewers [[spoiler: (minus the whole Lovecraftian horror element)]].
** After the term "Trap" became internet slang for an AttractiveBentGender character Fred's magazine ''Traps Illustrated'' takes on a whole new interpretation.
** Velma's counterpart of the Original Mystery Inc., Cassidy Williams, is [[BlackAndNerdy African American]]. In ''WesternAnimation/{{Velma}}'', the titular character [[RaceLift is the same race]] as Cassidy.
* HollywoodHomely: In "The Creeping Creatures", the landlady refuses to 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.
** At one point, [[IWasQuiteALooker Velma's mother shows her a photo of her in her youth]] and mentions that she was the subject of a number of pining hearts, to which Velma responds with genuine shock because she doesn't understand how her mother could've attracted so many men if [[GenerationXerox her daughter looks just like her]] -- as in, she's calling them both ugly.
* IKnewIt:
** Judy Reeves is Fred's mother, as the flashbacks in Season 1 depicted her as having a StrongFamilyResemblance to Fred. Also to a lesser extent, Brad Chiles is Fred's real father. The Season 1 finale would confirm this.
** Cassidy Williams and Angel Dynamite have some sort of relation, possibly because they're the same person. This was confirmed near the end of Season 1.
** Mayor Jones being divorced from Fred's mother (or more accurately, she left him). Confirmed in "[[Recap/ScoobyDooMysteryIncS1E23AHauntingInCrystalCove A Haunting in Crystal Cove]]", or at least that's what his cover story was.
** Mayor Jones is involved in the show's MythArc via the disappearance of the original Mystery Incorporated, and is not a trustworthy figure.
** Betrayal broke apart the original Mystery Incorporated because of Pericles.
* 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?" 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.]]
* LessDisturbingInContext: ''Mystery Incorporated'' is often brought out of context (usually on Website/{{Tumblr}}'') to talk about its ShockingMoments coming from a reboot of a beloved children's show.
** Scooby [[spoiler:being a descendant of a species of {{Eldritch Abomination}}s seems to evoke the image of Scooby being an incomprehensible interdimensional monster to anyone that hasn't seen the show, even though he's otherwise physically depicted to be a normal cartoon animal and his ancestry only mainly affects him by making him more sapient than regular animals.]]
** Marcie [[spoiler:getting killed in the first part of the series finale [[https://deathishauntedbyhumans.tumblr.com/post/175057685566/what-are-your-thoughts-on-scooby-doo-hot-dog-water is quite a popular post on Tumblr]] due to Marcie being an AmbiguouslyGay character (which has earned her an EnsembleDarkhorse status, even among FanworkOnlyFans) getting killed off in a WhatDoYouMeanItsForKids manner. As shown in the post, this has led to accusations of the show performing a BuryYourGays, when it's actually a subversion as the ''entire side cast'' is killed in the second part (many of which are straight as well as at least one AmbiguouslyBi character and a confirmed asexual character) but everyone gets revived anyways.]]
* MagnificentBastard: [[spoiler:[[MayorPain Mayor Fred Jones Sr.]] is secretly the Freak of Crystal Cove, the ArcVillain for season 1 and arguably the gang's most personal enemy. Decades ago Jones came to Crystal Cove in search of its fabled treasure, and to do this used the Mystery Inc. of his time to find pieces of the Planispheric Disc for him. In league with their mascot Professor Pericles, Jones blackmailed the gang with forged documents to run them out of town, then promptly doubled on Pericles and successfully framed him for the deed. Because of Jones' plans, Pericles--no idle schemer himself--rots in prison for eighteen years, while Jones becomes Mayor of Crystal Cove. When Brad Chiles and Judy Reeves attempted to return years later, Jones kidnapped their baby as leverage to drive them off. Jones would name this baby "Fred" and for the next eighteen years of his life gradually [[LimaSyndrome comes to love him as his own son]], to the point where he scuttles his own getaway to save Fred's life. Even after being arrested, Jones Sr. manages to help one-up Pericles again, and he ends as one of the show's few recurring villains to overcome the curse on his own, reconciling with Fred in the Sitting Room with pride and dignity.]]

* MemeticMutation: This being an entry in a childhood classic franchise, this was expected. The amount of ComedicSociopathy, [[LeaningOnTheFourthWall fourth-wall jokes]], and [[ContinuityLockout the heaviness]] [[ItMakesSenseInContext of context]] in this show only served to increase this, [[FanworkOnlyFans most of the people who hear of these jokes have little to no exposure]] to ''Mystery Incorporated'' due to the show not being as well-known as previous incarnations. Most often, these jokes are screencaps from the show.
** The explanation for Scooby being a TalkingAnimal? [[spoiler:[[CosmicHorrorStory Alien gods]].]]
** Internet culture a few years after the show ended didn't hesitate to have fun with Fred's exaggerated love of traps in this continuity.
** Comparisons to ''VideoGame/Persona4''. Both feature a group of AmateurSleuth teenagers uncovering a supernatural mystery involving monsters, [[spoiler:even ending with a fight against a god and winning it via the PowerOfFriendship]], among other things.
** Fred and Daphne expressing horror at a statue of Scrappy-Doo in the museum, [[TakeThatScrappy saying that they vowed to forget he existed.]]
** Fred saying to Odnarb in "The Wild Brood" that [[TheyCallMeMisterTibbs he goes by "Fred"]], unless they're dating, then it's "Freddie". Later in "All Fear the Freak", [[HoYay Shaggy calls him "Freddie".]] And before that, in "The Menacing Manticore", Velma calls him "Freddie"... and in "In Fear of the Phantom", [[InterspeciesRomance Scooby has called him "Freddie" too]]... [[{{Polyamory}} interesting]].
** [[https://i.ytimg.com/vi/qzTOQOdYKwY/hqdefault.jpg This]] screencap of Scooby wearing PoweredArmor with a Gatling gun. It's [[SugarWiki/MomentOfAwesome even cooler]] [[ItMakesSenseInContext in context.]]
** The {{fanon}} that Velma was attracted to other women strengthened with her AmbiguouslyGay relationship with Hot Dog Water.
** Mayor Jones' laziness in "The Creeping Creatures" and "A Haunting In Crystal Cove" being relatable.
--->'''Mayor Jones:''' I already got the recliner in the recline position. There's no going back from that. ''[sips cup of juice]''\\
'''Mayor Jones:''' ICantHearYou, I'm too comfortable. ''[pulls up blanket]''
** Happy tapioca, due to the Website/UrbanDictionary definition[[labelnote:Explanation (NSFW)]]Not only is the receiver submerged in tapioca pudding, but they also receive anal sex. For the record, this definition was created after the joke was made, so this is {{fanon}}.[[/labelnote]] and the "Unnecessary Censorship" segment from ''Series/JimmyKimmelLive''.
** This exchange:
-->'''Shaggy:''' But, like, what if they want to eat my brains?\\
'''Velma:''' [[DeadpanSnarker It'll be a light meal.]]
** The LampshadeHanging about [[MsFanservice Obliteratrix's]] {{stripperific}} outfit being AwesomeButImpractical for weapon storage.
** "Shaggy, are you cheating on me?" - said by ''Scooby''.
** "I have feelings, world; for traps and Daphne! I'm a guy no more!"
* MoralEventHorizon:
** Professor Pericles goes over it the moment he shows he's willing to [[spoiler: kill Ed Machine]] just to "send a message" to Mr. E. [[spoiler:And this is ''before'' we learn that he'd conspired with Mayor Jones and sold out his friends in order to get the treasure.]]
** Brad and Judy [[spoiler:getting plastic surgery to look like their own ''son'' and his girlfriend to trick the gang. Not to mention burning down City Hall, being compliant in enslaving the people of Crystal Cove while being more concerned about being unable to undo their plastic surgery, and letting Pericles kill Hot Dog Water.]]
** The [[spoiler: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 Anunnaki ever]]. It's being the cause of corruption of ''all villains'', even Professor Pericles, stands out too.
* {{Narm}}:
** At the end of Season 1, Scooby ending his promise to get the gang back together and go after Pericles with "or my name isn't Scooby Dooby Doo!" either undercuts the tension entirely or [[NarmCharm just sort of works depending on who you are.]]
*** To a similar extent, Fred questioning the motive of [[spoiler:Mayor Jones]] with "All this for a treasure no one's even sure exists?" can be derailed or enhanced for anyone fixated on [[MemeticMutation the way Fred pronounces "treasure".]]
** Even as the plot gets very dark, they continue to refer to Marcie as "Hot Dog Water", killing the tension.
* NeverLiveItDown:
** [[MemeticMutation In a memeworthy type of way]]. The explanation for why Scooby is a TalkingAnimal and why no one treats him special. [[spoiler:In ancient times, an alien race called the Annunaki used animals as vessels to talk to human beings, and their descendants became talking animals.]]
** The controversial characterizations of the gang, either because it's memetic (often Fred for his obsession with traps) or a drastic departure from how they were previously characterized, particularly the Velma/Shaggy romance subplot and [[FriendVersusLover Velma & Scooby fighting over Shaggy]], since Velma's TookALevelInCynic went against her usual NiceGirl depiction, Shaggy/[[WesternAnimation/ScoobyDooAndTheAlienInvaders Crystal]] is usually the FanPreferredCouple, and previous works never hinted that Velma/Shaggy was romantic in any manner. The creators have even said that Velma and Shaggy were ''intentionally'' written as a bad couple, with the implication being that [[WordOfGay Velma was a closeted lesbian]] and her clumsy, clingy romance was basically her attempt to prove otherwise. However, this has softened up considerably after the release of ''WesternAnimation/{{Velma}}'', wherein their counterparts are frequently viewed as bearing so little resemblance to the original characters beyond superficial characteristics that this show's changes look more tame in comparison.
* NightmareRetardant: The [[spoiler: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 degrees in frightening.
* OlderThanTheyThink:
** Velma's parents previously appeared [[FlatCharacter non-descriptively]] in ''WesternAnimation/APupNamedScoobyDoo'', so if you're into compositing things together, you might as well just consider them the same characters. The ''Those Meddling Kids'' commercials from the '90's briefly showed us Velma's parents as they would have appeared in the original show, and funnily enough, they actually resemble each other quite a bit bar age and hair color.
** Also from ''Those Meddling Kids'' commercials, Daphne's father in that version was also voiced by Creator/FrankWelker, using the same voice he uses for Mr. Blake in ''Mystery Incorporated''.
* 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.
** The series did this to Daphne, whose character wasn't very well defined, as depending which Scooby-Doo series you were watching she could have been an ActionGirl, a FauxActionGirl, a fashionista, just as bland as Fred, the [[OnlySaneMan only one normal]] or the DamselInDistress. In this series, she's a [[TheDitz ditzy]] but lovable girl who is perfectly competent, if a little insecure. This personality tweak was so well received that it was kept up to the newest DTV Scooby movies.
** 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 [[CosmicRetcon Cosmic Retconned]] self pulls him from being hated.]]
* RetroactiveRecognition: Creator/ChristianLanz is the voice of [[spoiler:villains-of-the-week]] Fernando el Aguirre and Prof. Enrique Andelusossa, and would later be better known for his roles as [[WesternAnimation/ElenaOfAvalor Chancellor Esteban]] and [[VideoGame/CallOfDutyBlackOps4 Diego Necalli]].
* RomanticPlotTumor: Many fans of this show agree that the romance plots which are more prevalent in the first season are the weakest part of the story. [[TookALevelInJerkass Fred and Daphne constantly go back and forth if they want to be in a relationship or not]] as Fred constantly puts his love for traps before Daphne and is more interested in dating Daphne once she doesn't return his feelings in Season 2. Not to mention, both Scooby and Velma really TookALevelInJerkass when it comes to Shaggy dating Velma, as they are both very possessive with him. Scooby is against Shaggy being in a relationship, and Velma constantly acts like a self-centered woman-child when she's dating Shaggy.
* SignatureScene:
** The "Trap of Love" concert. Overlaps with BestKnownForTheFanservice.
** The final battle being [[spoiler:against an EldritchAbomination]], though it's less that people have actually watched it themselves and more due to word of mouth caused by shock that a ''Scooby-Doo'' cartoon ''went there''.
** Word went around that [[spoiler:Hot Dog Water -- a friend of Mystery Incorporated -- gets ''shot to death'' by Nazi robots]].
* SurprisinglyImprovedSequel: Considering all the ''Franchise/ScoobyDoo'' stuff that was coming out after ''WesternAnimation/WhatsNewScoobyDoo'' ended.
* TakeThatScrappy: In episode 20 of Season 1, Daphne and Fred notice two statues of [[WesternAnimation/The13GhostsOfScoobyDoo Flim-Flam]] and Scrappy in the Spook Museum. Daphne comments on how Flim-Flam, a character who was so hated that he became the Scrappy in a series that actually had Scrappy in it, was busy serving 20-years-to-life in prison for his ConMan schemes. When they notice Scrappy they both shudder and mention how they swore to never speak of him again (possibly referencing the events of the [[Film/ScoobyDoo live-action film]]).
* 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".
* TheyWastedAPerfectlyGoodCharacter:
** Mayor Jones is DemotedToExtra after Season 1, [[spoiler:so his actions and strained relationship with Fred are barely touched upon, though hastily found closure in one of the final episodes of the show.]]
** The Blake sisters are [[FlatCharacter flat characters]] that have little to no impact in the show, which can be disappointing considering the other members of the Gang don't have siblings in this version. Delilah only has one major scene, which is played for laughs, and Daisy also only has a minor role in one episode.
** [[spoiler:While a cool concept for the origins of Crystal Cove and Mystery Inc, the Nibiru Entity himself doesn't get any screentime until the GrandFinale and little characterization beyond "evil and wants to eat everything". His creation of Mystery Inc's foes (and the reason for the supernatural creature themed disguises) is also never explored beyond a throwaway line by Velma.]]
* TheyWastedAPerfectlyGoodPlot:
** A few anime fans were disappointed that "When the Cicada Calls" didn't make any further [[ShoutOut Shout Outs]] to ''VisualNovel/HigurashiWhenTheyCry'' besides the episode name, the local festival, the victims being catatonic after being attacked, an environmentally-unfriendly company harming the town, and the hospital patient that flatlines from a heart attack. But then again, this is probably as far as the show can go when referencing something as violent and bed-wetting as ''Higurashi''.
** The Season 1 finale ending with [[spoiler:Mystery Incorporated being divided is a TenMinuteRetirement.]]
** Brad & Judy and Mayor Jones never have a confrontation. The nearest they ever get to each other in the present day is "Gates of Gloom" by a few yards, but still in different scenes -- Jones' appearance is even just TheCameo. Brad and Judy never even talk about Jones besides once in "Hodag of Horror" when they explain that [[spoiler:he threatened to hurt Fred if they didn't leave. Similarly, Ricky and Cassidy never talk to Jones either besides the former expressing disdain of him (though he didn't know that Jones and the Freak were the same person at the time) and the latter showing disgust when it turned out Jones was the Freak.]]
** The life and adventures of the original Mystery Incorporated (and other past mystery-solver groups) are not delved into, which could have served to parallel the present Mystery Incorporated's story throughout the show.
** Mayor Nettles is revealed to be former Air Force, but she never gets to properly establish herself as an ActionGirl and it mostly just serves as a {{Handwave}} for her to pilot a helicopter to accompany the gang in one episode.
** The ending, though it's understandable as there wasn't enough time left in the episode to further delve into it. [[spoiler:The CosmicRetcon ResetButtonEnding means that almost everyone has a perfect life, but no one except for the gang remembers the original timeline. The gang also feel like [[StrangerInAFamiliarLand strangers in a familiar land]], since the people they're surrounded by are not the same people they knew and they don't remember any of the good experiences they've had in this new timeline (''especially'' regarding Fred, who got to grow up loved as Brad and Judy's son), but this identity crisis is not touched upon any further.]]
** While the show's [[MythArc overarching mystery]] is considered to be one of its strongest attributes, it is hampered somewhat by the fact that almost every episode still follows the general ''Scooby-Doo'' formula, which can make the show feel somewhat repetitive for viewers who are mainly interested in the MythArc. Making things worse is the fact that, as per WordOfGod, the show was intended to be [[BetterOnDVD binge-watched]], and yet the episodic nature of its storytelling severely bogs down the show's pacing.
** In ''Nightmare in Red'' the gang arrives at a room containing [[spoiler:the good parts of a number of other people who have been influenced by the [[HatePlague curse]] of the treasure, including Cassidy, Brad and Judy, the Darrows, and others. It presented an opportunity to get to know more about them at their best, but the only ones the gang ever speaks with are Mayor Jones and the captain of the conquistadors]].
* 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 ones 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.
** It's softened a little when you remember that [[spoiler: in the original timeline]] they all graduated Darrow University at ''thirteen'', so it's possible they are all destined for the same or similar careers, just not at the same ridiculously young ages that made Daphne feel comparatively inadequate [[spoiler: in the original timeline.]] (Daisy, for example, would probably still be in med school at the time when the series leaves off.)
* TheUntwist: 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}} Oktoberfester]] 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.]]
* WhatDoYouMeanItsForKids: This is the most violent and terrifying iteration of ''Scooby Doo'' since ''[[WesternAnimation/ScoobyDooOnZombieIsland Zombie Island]]'' and in some aspects even worse. The show touches on things like parental abandonment and child kidnapping, there's conquistador massacres in the backstory, the gang fight literal ''Nazi robots'' [[spoiler:who machine gun one of their teenage friends to death, and by the final episode every single person in Crystal Cove has been killed by an EldritchAbomination that wants to devour the entire universe]]. The suggestive aspects of the show are also jacked up, from Fred's obsession over his "Traps Illustrated" magazine to the repeated blatant hints Velma wants to take her relationship with Shaggy to the next level. To say the themes of this show get a little intense for a TV-Y7 show--let alone an iteration of Scooby Doo--is putting it extremely mildly.
* TheWoobie:
** Fred. Fred. Fred. The Season 1 finale reveals that [[spoiler:he's a kidnapping victim, abducted by Mayor Jones as a baby and taken away from his real parents -- parents who were into mystery-solving like him -- as leverage to keep them away from Crystal Cove forever for a treasure that might not even exist. He's been lied to his entire life by a man who didn't even support him because he was always his enemy. It's no wonder why he decides to leave town to find his parents. 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.]]
** Hot Dog Water/Marcie in Season 2, who gets accepted into Mystery Incorporated at the beginning and finally gets to have friends, only to be kicked out when Daphne rejoins ([[KickTheDog "It's always just been the five of us..."]]). The gang never act on her status as SixthRanger, so they don't pursue her help during their investigations, but she plays one or two important minor roles later until [[spoiler:being killed in a HeroicSacrifice]] at the end of the show. Fortunately, [[spoiler:she's brought back to life after the universe resets and [[EarnYourHappyEnding she gets to keep her friends, especially Velma]].]]
** Angel Dynamite. [[spoiler:Like her friends, they were forced into hiding to keep their families safe after the Freak (really, Pericles and Fred Jones, Sr.) threatened to frame their parents for crimes they didn't commit just to keep the kids from finding the treasure for themselves. After spending the last decade or so away from home, Ricky/Mr. E drags her back into the mystery and to spy on the new Mystery Incorporated. In spite of Mr. E's plans, Angel tries her damnedest to keep the kids safe and she's ultimately the only one from the original team that still cared enough to do so. She ends up paying for this with [[HeroicSacrifice her life]].]]
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