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  • Acceptable Targets:
    • In the first episode, the culprit is a teacher who was trying to rob a bank because he isn’t paid much, which is a Take That! towards the American public education system for underpaying teachers and giving little funding to public schools.
    • Teen horror movies. The show's romance plots and take on horror are parodies of what you’d find in this genre.
  • Accidental Innuendo:
    • Traps Illustrated, if you know what the word trap can also mean.
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    • 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.
  • Alternative Character Interpretation:
    • 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 love Shaggy or 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 Ship Tease 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?
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    • Shaggy's love for Vincent Van Ghoul's horror movies suggests that he is a Nightmare Fetishist who continues to be a member of the gang because he derives cheap thrills from being scared out of his 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 Scooby seemed to think that Velma's romantic relationship with a threat to his "best buddy" relationship with his nonromantic Heterosexual Life-Partner, Shaggy, adds to it as well.
  • Angst Aversion: Can bring about this to some, but more notably the show received this from franchise creators Joe Ruby and Ken Spears, who despised it for being too dark and cynical.
  • Angst? What Angst?:
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    • At the end of "The Dragon's Secret", upon learning that Mai Le was 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 Everybody Laughs Ending. Probably since the episode wasn't supposed to add to the plot and the writers didn't want to repeat another break-up arc.
    • The ending. A Cosmic Retcon 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 Parents 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 Ripple Effect-Proof Memory will eventually let the gang remember both timelines to make adjusting to this timeline easier.
  • Author's Saving Throw: "Dance of the Undead" switched the Hex Girls back to their original outfits (with a tongue-in-cheek reference to the complaints about them), and featured them prominently assisting Shaggy and Scooby in defeating the Ska Zombies.
  • Badass Decay: Mr. E's actions never quite stop being threatening or competent, (with the exception of one instance of being Out-Gambitted) but you have to admit knowing he's grotesquely overweight and actually playing his background keytar music doesn't do a whole lot for his air of menace, and it gets particularly bad when he ends up being personally intimidated by a confrontational Shaggy at one point.
  • Base-Breaking Character:
    • 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 she's a product of her environment and she does undergo Character Development, while the other side argues that Velma being unsympathizing is a departure from her usual Nice Girl depictions.
    • The new look of the Hex Girls is very divisive, as well. A future episode has them back in their original outfits, however along with a line stating that there were people who liked their old looks.
  • Big-Lipped Alligator Moment:
    • "Mystery Solvers Club State Finals" has Principal Quinlan, who seems to exist for the sole sake of Does This Remind You of Anything? Their First Time. A Nervous Wreck, she makes Ambiguously Gay comments towards Angel, and that along with her becoming Hotter and Sexier when she has an Adrenaline Makeover after giving "CPR" to Speed Buggy come off as her being inexperienced with romance and sex. 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 One-Shot Character, so this never comes up again in any way.
    • 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 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 the Entity's influence, but it's never made clear.
    • 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.
  • Broken Base:
    • The amount of Crosses the Line Twice/Comedic Sociopathy jokes. Some are funny, but are others problematic? And if you do consider these jokes as problematic, are these properly addressed?
    • If the Darker and Edgier and Denser and Wackier 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?
  • Cargo Ship: Fred and traps. Seriously, he can't walk past a net or a cage without swooning over it.
  • Complete Monster: The Nibiru Entity is a member of a normally benevolent inter-dimensional alien race called the Anunnaki, which considers him the most evil member of their entire species. He's spent untold centuries corrupting and manipulating everyone around him, especially the team pets 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 Professor Pericles, who 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 Hell on Earth 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.
  • Continuity Lockout: 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 Previously On… segments. The show's ending, however, at 52 episodes and 2 seasons, may mitigate this. It is nonetheless a lot better in one sitting.
  • Creepy Awesome: Professor Pericles. Creepy? Oh yeah. Awesome? Udo Kier makes it so.
  • Crosses the Line Twice:
    • 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 You Have GOT to Be Kidding Me! 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... He seems embarrassed about owning some issues, but he claims he only reads it for the articles (which may be true).
      • And his real 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, we kid you not:
    Scooby: Shaggy... 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?! This isn’t some reality show!
    • Mayor Jones when he drops off Fred to meet his old college fraternity:
  • Draco in Leather Pants: Misinterpretations of all of Fred's parents have led to some viewing Mayor Jones as the better of the three solely because of his Papa Wolf 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 Word of God, the intent was to make Brad and Judy look so despicable that Jones would be sympathetic 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 being victims of the Entity's curse just as Jones was. Word of God 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.
  • Ensemble Dark Horse:
    • Marcie "Hot Dog Water" Fleach due to being the gang's Sixth Ranger and especially all of her Les Yay with Velma. Even detractors have cited her as one of the best parts of the show and her horrifying demise at the hands of Pericles' Nazi robots made serious waves in the fandom.
    • Cassidy Williams/Angel Dynamite for her cool personality and being the Token Good Teammate 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 recieved.
    • Alice May, for her looks.
    • Not to mention, Harlan Ellison for fairly obvious reasons.
    • Sheriff Stone, by virtue of being voiced by Patrick Warburton.
    • Mayor Jones for being a Bunny-Ears Lawyer who is revealed to be a Manipulative Bastard.
    • Mayor Nettles, for being attractive, understanding, and competent.
    • Delilah Blake for being a Cool Big Sis to Daphne and being voiced by Jennifer Hale.
  • Epileptic Trees:
    • 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. Ultimately, 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 things becoming undone once the Entity is defeated. General consensus was that either there would be a Reset Button Ending 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 Myth Arc would come back to life. It ended up being a Cosmic Retcon in which everyone is happy with little to no catches.
  • Evil Is Cool:
    • Professor Pericles, the chief Big Bad, is easily the most popular and memorable villain in the show for this reason.
    • 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 Clancy Brown certainly helps.
  • Evil Is Sexy:
    • Alice May, especially as Obliteratix in episode 25.
    • For some people, Mayor Jones, apparently.
    • Apparently, a few circles find Brad and Judy a bit on the foxy side...
  • Fanfic Fuel: Just what happened to Scrappy that made Mystery Inc. agree to never mention him again?
  • Fanon:
    • Velma confiding to Marcie about the events of the show in the new timeline, due to her status as The Sixth Ranger 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 he's the only character that says they have a 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 the situation about all of his parents in the new universe.
  • "Funny Aneurysm" Moment:
    • 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. He gets eaten by the Entity at the end of the show, but it's played for Nightmare Fuel/Tear Jerker.
    • "Mystery Solvers Club State Finals" is an amusing episode, and the reveal of Mudsy as the villain is rather funny. Season 2 then starts to imply that the animal or any unique companion to a mystery-solving group will turn evil because of the mystery of Nibiru.
  • Genius Bonus:
    • 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 Conan the Barbarian novels, who really was a correspondent of Lovecraft's while he was in his twenties.
  • Growing the Beard: 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 and develop, and focusing on the main Story Arc with goofy episodes in-between.
  • Harsher in Hindsight: In "When the Cicadas Cry", Mayor Jones entertains the idea of having Fred getting Eaten Alive by the Cicada Monster for a boost in tourism. At the end of Season 1, he nearly kills him in a confrontation but can't bring himself to do it, and at the end of the show, he himself gets eaten alive by a real monster.
  • He Really Can Act: While Frank Welker 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 especially with his parents' involvement. With the Season 1 finale in particular, his anger and grief at 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.
  • Heartwarming in Hindsight:
    • Angel helping the mascots save their friends in "Mystery Solvers Club State Finals", because she herself is the Token Good Teammate 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.
    • Casey Kasem Passing the Torch of being the voice of Shaggy to Matthew Lillard while playing as Shaggy's father became this when his final lines in the show where telling Shaggy how proud he is of him before he would pass away shortly after in real life.
  • Hilarious in Hindsight:
    • 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.
    • Matthew Lillard becoming the new voice of Shaggy despite being threatened by the animated Shaggy and Scooby in Looney Tunes: Back in Action for his performance in the first live action movie.
    • 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. Angel is Cassidy.
    • Years after this show concluded, a popular meme would be Shaggy being a badass (due to Legend of the Phantosaur), followed up by the meme of his source of power being because he's an Eldritch Abomination, is this trope, since the show reveals that Scooby is also an Eldritch Abomination (to some extent).
    • 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 Vietnam War.
    • When visiting the Sppok 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 Scooby-Doo! and the Curse of the 13th Ghost, 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.
  • Hollywood Homely: 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 Hollywood Homely has became a Running Gag, almost at Meg Griffin's levels.
  • Jerkass Woobie:
    • Velma. You can't help but feel sorry for her when Shaggy picks Scooby over her. Granted, Shaggy probably wasn't a good match for her anyway... 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 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.
    • 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 Redemption Equals Death, 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.
  • Less Disturbing in Context: Mystery Incorporated is often brought out of context (usually on Tumblr'') to talk about its Shocking Moments coming from a reboot of a beloved children's show.
    • Scooby being a descendant of a species of Eldritch Abominations 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 getting killed in the first part of the series finale is quite a popular post on Tumblr due to Marcie being an Ambiguously Gay character (which has earned her an Ensemble Dark Horse status, even among Fanwork-Only Fans) getting killed off in a What Do You Mean, It's for Kids? manner. As shown in the post, this has led to accusations of the show performing a Bury Your Gays, 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 Ambiguously Bi character and a confirmed asexual character) but everyone gets revived anyways.
  • Memetic Mutation: This being an entry in a childhood classic franchise, this was expected. The amount of Comedic Sociopathy, fourth-wall jokes, and the heaviness of context in this show only served to increase this, 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 Talking Animal? 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. A meme that mostly originated from the growing anime community at the time was jokes about the Wholesome Crossdresser trope and transgender people being used for Moe or Fanservice bait in anime, labelled as "traps"note 
    • Comparisons to Persona 4. Both feature a group of Amateur Sleuth teenagers uncovering a supernatural mystery involving monsters, even ending with a fight against a god and winning it via the Power of Friendship, among other things.
    • Fred and Daphne expressing horror at a statue of Scrappy-Doo in the museum, saying that they vowed to forget he existed.
    • Fred saying to Odnarb in "The Wild Brood" that he goes by "Fred", unless they're dating, then it's "Freddie". Later in "All Fear the Freak", Shaggy calls him "Freddie". And before that, in "The Menacing Manticore", Velma calls him "Freddie"... and in "In Fear of the Phantom", Scooby has called him "Freddie" too... interesting.
    • This screencap of Scooby wearing Powered Armor with a Gatling gun. It's even cooler in context.
    • The fanon that Velma was attracted to other women strengthened with her Ambiguously Gay relationship with Hot Dog Water.
    • Mayor Jones's 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: I Can't Hear You, I'm too comfortable. [pulls up blanket]
    • Happy tapioca, due to the Urban Dictionary definitionExplanation (NSFW)  and the "Unnecessary Censorship" segment from Jimmy Kimmel Live!.
    • This exchange:
    Shaggy: But, like, what if they want to eat my brains?
    Velma: It'll be a light meal.
  • Moral Event Horizon:
    • Professor Pericles goes over it the moment he shows he's willing to kill a man just to "send a message" to Mr. E. 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 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 Nibiru Entity gets one when, after it is freed, it 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 just sort of works depending on who you are.
  • Never Live It Down:
  • Nightmare Retardant: The 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.
  • Older Than They Think:
    • Velma's parents previously appeared non-descriptively in A Pup Named Scooby-Doo, 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 Frank Welker, using the same voice he uses for Mr. Blake in Mystery Incorporated.
  • Rescued from the Scrappy Heap:
    • This series has done this for Fred. He used to be the Trope Namer for Standardized Leader (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 Action Girl, a Faux Action Girl, a fashionista, just as bland as Fred, the only one normal or the Damsel in Distress. In this series, she's a 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 he was revealed to be the Freak of Crystal Cove, the first season's Big Bad, meaning that one was supposed to dislike him, and he fell into Love to Hate as a truly nasty Knight of Cerebus, or if not then Hate Sink. He was rescued again when it was revealed that 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 Retconned self pulls him from being hated.
  • Retroactive Recognition: Christian Lanz is the voice of villains-of-the-week Fernando el Aguirre and Prof. Enrique Andelusossa, and would later be better known for his roles as Chancellor Esteban and Diego Necalli.
  • Romantic Plot Tumor: Many fans of this show agree that the romance plots are the weakest part of the story. 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, and then Fred once again goes back to loving traps more once Daphne is interested in him again. Not to mention, both Scooby and Velma really Took a Level in Jerkass when it comes to Shaggy dating Velma, as they are both very possessive with him. Scooby is against Shaggy being in a relationship and frequently refers to him in third person as "My Shaggy", and Velma constantly acts like a self-centered woman-child when she's dating Shaggy.
  • Signature Scene:
    • The "Trap of Love" concert. Overlaps with Best Known for the Fanservice.
    • The final battle being against an Eldritch Abomination, 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 Hot Dog Water — a friend of Mystery Incorporated — gets shot to death by Nazi robots.
  • Surprisingly Improved Sequel: Considering all the Scooby-Doo stuff that was coming out after What's New, Scooby-Doo? ended.
  • Take That, Scrappy!: In episode 20 of season one, Daphne and Fred notice two statues of 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 Con Man 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 live-action film.
  • They Changed It, Now It Sucks!:
    • 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".
  • They Wasted a Perfectly Good Character:
    • Mayor Jones is Demoted to Extra after Season 1, 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.
    • Mayor Nettles is revealed to be former Air Force, but she never establishes herself as an Action Girl and it mostly just serves as a Handwave for her to pilot a helicopter to accompany the gang in one episode.
    • The Blake sisters are 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.
  • They Wasted a Perfectly Good Plot:
    • A few anime fans were disappointed that "When the Cicada Calls" didn't make any further Shout Outs to Higurashi: When They Cry 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 bedwetting as Higurashi.
    • The Season 1 finale ending with Mystery Incorporated being divided is a 10-Minute Retirement.
    • Brad & Judy and 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's appearance is even just The Cameo. Brad and Judy never even talk about Jones besides once in "Hodag of Horror" when they explain that 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.
    • The ending, though it's understandable as there wasn't enough time left in the episode to further delve into it. The Cosmic Retcon Reset Button Ending means that almost everyone has a perfect life, but no one except for the gang remembers the original timeline. The gang also feel like 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 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 Myth Arc. Making things worse is the fact that, as per Word of God, the show was intended to be 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 the good parts of a number of other people who have been influenced by the 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.
  • Unintentionally Sympathetic: Daphne's sisters losing their successful careers and marriages in the new timeline. It's supposed to be something of a Break the Haughty moment where those who succeeded at Daphne's expense were punished while she was rewarded, and Daphne's status as The Unfavorite 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.
  • The Un-Twist:
    • "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?
    • "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 Hot Dog Water was the Manticore. And since they bring it up in season 2 it could also be a Late-Arrival Spoiler.
    • The entire point of "The Gathering Gloom"'s mystery. The rest of the gang chides Velma for immediately suspecting Count Evallo as the Monster of the Week, and begin investigating the incredibly friendly 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.
    • In "The Song of Mystery", 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!
  • What an Idiot!:
    • 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" might have gotten away with it, too, if he hadn't staged an attack in broad daylight!
      • The intention might have been to lead someone to trapped victims who needed medical help.
    • The whole gang still not having realized the gaping hole in Alice May's Daddy's Little Villain con by the time of her reappearance.
    • Season 2, Episode 9: 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. Their whole reasoning behind their Face–Heel Turn 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 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?
    • Professor Pericles gets this the worst of anyone when he willingly lets the Evil Entity consume him, and yes Pericles even uses the term "consume" to describe the act, and then expects to be in control of the Entity's power afterwards and not, you know, the thing doing the consuming. Sure enough he has a few seconds of control before the Entity devours his soul and reshapes his body into one more fitting to it's tastes.
  • What Do You Mean, It's for Kids?: This is the most violent and terrifying iteration of Scooby Doo since 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 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 Eldritch Abomination 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.
  • The Woobie:
    • Fred. Fred. and Fred. The Season 1 finale reveals that 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. Daphne's moved on, the plan failed, The Bad Guy Wins, oh, and he's been living as a hobo for a while now... someone give him a hug. Then his parents move in, and they're just as good as one could hope! Until they join Mr. E and Professor Pericles. And Fred moves out of his house, instead of kicking them out.
    • Don't forget Daphne. 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 ("It's always just been the five of us..."). The gang never act on her status as Sixth Ranger, so they don't pursue her help during their investigations, but she plays one or two important minor roles later until being killed in a Heroic Sacrifice at the end of the show. Fortunately, she's brought back to life after the universe resets and she gets to keep her friends, especially Velma.
    • Angel. 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 damndest 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 her life.

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