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  • Badass Decay: Bishop appears to suffer from this in Fast Forward, but redeems himself in "Day of Awakening."
  • Base Breaker: Some people dislike Quarry for not looking pretty and humanistic, others find her fascinating for her dark backstory.
  • Complete Monster: The Shredder does some rather horrible things in the series--not only does his backstory indicate that he's responsible for the death of millions, this is actually small change compared to what he attempts in Turtles Forever.
  • Ear Worm: The Theme Songs.
  • Ensemble Darkhorse: Hun and Bishop.
    • Also, Usagi and Gen are both really popular and tend to steal the show whenever they show up.
  • Evil Is Cool: Shredder.
  • Fanon Discontinuity: For some fans, Fast Forward and Back to the Sewer seasons.
  • Fridge Brilliance: After his defeat in "The Shredder Strikes, Part 2," Shredder makes it a point of going after the Turtles and eliminating them. Seems like common sense and simple revenge, right? But then "Timing is Everything" showed Shredder after his first defeat facing the more-skilled Turtles by way of time travel. He knew they would become more powerful and eventually defeat him (as Raph says), so his motives weren't pure revenge.
  • Fridge Horror: Possibly mixed with Harsher in Hindsight. An un-produced episode of the Ninja Tribunal season was going to reveal that Hun and The Garbageman were conjoined twins separated at birth by a back-alley surgeon. That was horrific enough that it got the episode scraped by the network, but it gets even worse when who realize that it was hinted at two seasons earlier during "Same As It Never Was." Brings the Shredder's punishment of Hun and Stockman to an all-new level of "apropos."
  • Fridge Logic: Rare in-universe example during Fast Forward. When the turtles find what appears to be April's journal, from which Cody learned about the turtles, they all sneak in to read it late at night. However, as they get to the end of Raphael's story, they notice contradictions between the story and what they already know about recent history. Just then, Cody and Splinter enter and reveal that they had replaced the journal with a fake to teach the turtles a lesson.
  • Hilarious in Hindsight:
    • In "Exodus", it was promised "One of these characters will never be seen again.", and after the episode, Ch'rell is banished to an ice planet, likely never to be seen again... That is, until Turtles Forever, and even earlier than that, in the first Back To The Sewers episode, and they even planned on an arc involving "The Shredder Wars" had Back To The Sewers got another season, either way, the promise clearly wasn't kept.
    • Same as it Never Was has April try and take out Karai with a rocket launcher. Why is this hilarious? In the CG film April is voiced by Sarah Michelle Gellar...BuffyTheVampireSlayer who infamously killed a demon with a rocket launcher.
    • The Fast Forward season with the turtles living among aliens could count as this, considering Michael Bay's announcement that the turtles will be aliens in his film.
  • Magnificent Bastard: Oroku Saki, Agent Bishop, and The Ninja Tribunal.
  • Moral Event Horizon: For the Shredder, this was the episode "Mission of Gravity", where we learned that not only is he willing to kill millions when it serves his purposes, he'd also do so when it wouldn't.
  • Nightmare Fuel: Baxter Stockman, especially the episode "Insane In The Membrane".
    • His return in Adventures in Turtle-sitting.
    • Shredder's reaction to Stockman's continued failures.
    • Same As It Never Was, the episode seemed to have been intentionally designed to be utterly terrifying, and probably to show exactly what the Shredder would do if he were to take over a planet, the results are, yet again, terrifying.
    • All of the series's newly-introduced mutants. If you're expecting anything remotely like Mona Lisa or whatnot, you'll be horrified at some of the horrid monsters the show introduced.
  • Only the Author Can Save Them Now: Several times, most notably with the resolution to the Demon Shredder arc.
  • Replacement Scrappy: The Demon Shredder. The Cyber Shredder is a borderline example, being a AI copy of the original with no really distinctive features on his own besides living inside cyberspace.
  • The Scrappy: Cody Jones is considered this.
  • Seasonal Rot: By Fast Forward, although some people would place it even earlier.
    • Really Season 4 was the high point with some complex and surprisingly well written arcs for both Leonardy and Michelangelo. The two retools made the show much more child friendly and typical (robots, digital realms, collect the clues saga), but Season 4 stands as a nice end to a good cartoon.
  • Straw Man Has a Point: Throughtout Season 4, Leonardo becomes increasingly hardened and more of a jerk than Raphael ever was. After the Turtles and Casey fail to stop a Purple Dragon convoy in "Dragons Rising," the trope is invoked as Leonardo delivers a pretty brutal "The Reason You Suck" Speech:

 Leonardo: Half! We stopped half and only because we got lucky! Is that good enough for you? Is it?! We're always one step behind! We act like a bunch of amateurs! How many times are we gonna get beaten before you guys wise up and realize this isn't a game?! (storms off)

Raphael: I hate to admit it, but he ain't wrong.

  • Tear Jerker: A few episodes. Especially any episodes involving Nano.
    • Kirby giving Donatello a sketch of him with a ray gun and final words: Don - "Life at best is bitter sweet." Take care of yourself. - Kirby
    • When "Insane In The Membrane" isn't flat-out terrifying you, it's making you sad when you watch Baxter's past.
  • They Changed It, Now It Sucks: Fast Forward gets accused of this a lot.
    • The entire 2003 series got accused of this by fans of the '80s cartoon, with complaints that they wished it was more like the "original" series. The irony being that the 2003 series, was far more faithful to the REAL original Turtles of the comics, than the '80s series ever was. Fan Dumb indeed.
  • Unfortunate Implications: Starlee's Space Jew family.
  • Villain Decay: Inverted, the Shredder managed to stay a dangerous antagonist, he even managed to top himself in every evil plan he committed, with the Utrom Shredder being considered the most dangerous of the bunch.
    • Hun himself though, seems to play it mostly straight, while he can fight the Turtles, he gets significantly more pathetic, while later seasons do try to avoid it, he ends up becoming a bigger loser, though, to be fair, in Back To The Sewers, he learned more techniques that allow him to fight the Turtles and even becomes a Crime lord... Doesn't stop them from learning to fight him again, although in Turtles Forever, he turns into a Turtle Monster, he ends up being so powerful that the Turtles can't lay a scratch on him.
    • Karai suffers this badly in season 4. From one appearance to the next, she goes from destroying the turtle's lair, all of their vehicles, and nearly killing 3 out 4 turtles and Splinter to playing and losing a rather humiliating game of keep away for a McGuffin against Leo and Mikey, including a sequence where they pick her up and drag her by the legs before throwing her out of an elevator shaft, in a manner more suiting Bebob and Rocksteady.
    • The Cyber Shredder, granted, it's the Shredder's data before Shredder became more and more Genre Savvy, but... His plans constantly fail and get repetitive, even when he does get out of Cyberspace.
  • Villain Sue: Bishop, due to the sheer ease that he manages to outfight the Turtles, Hun & Karai, his repeated elaborate escapes & the fact that even when he loses, he still wins in the grand scheme of things.
  • The Woobie: I can't be the only one who felt sorry for Nano in its first couple of appearances. Maybe that's why it got a happy ending after all.
    • You aren't, this Troper still cries in Nano's appearances.
      • To recap, in Nano's first appearance, it's defeated by getting dropped into a vat of molten steel, and survived, and only to get broken into pieces when returned. An AI that's only a child at heart and doesn't fully understand right from gets defeats more painful that what the Complete Monster villains in the series endure.
    • And let's not forget poor Dr. Stockman. This Troper has never felt so bad for a villain until "Adventures in Turtle-Sitting", in which , after being revived again, asks why Bishop doesn't let him rest in peace.
    • Donatello, arguably, he's dealt with some of the worst crap in this series, he's been in a Lotus Eater Machine where he's seen Angel die before his eyes, another where he's in a bad future, where he sees all of his brothers and learning all of his best friends have died, and was turned into a beast, at one point, life is rough on him.
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