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  • Alternative Character Interpretation:
    • The fact that despite being a genocidal maniac who wanted nothing more than to return to the stars to begin his conquest anew, Ch’Rell still decided to take in, raise, and train an orphaned human girl out of no reason other than simple altruism. This has left an impression on fans years after the series ended as they were left to debate his intentions and what this says about even the most vile incarnation of the character to date.
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    • In "I, Monster", during the end of Leonardo and the Rat King's fight, the Rat King leaped off an unstable piece of flooring which would've soon collapsed into a sea of rats below and landed on Leonardo. Considering how previously, Leonardo had saved him from a collapsing tower, was the Rat King genuinely trying to get away and coincidentally just happened to land on Leo, or was he still acting in a malicious manner and still trying to attack Leo and/or take Leo down with him? Evidently, Leo felt it was the latter, considering he retaliated by angrily kicking the Rat King into the ocean of rats in the lower floor.
    • In “Turtle X-Tinction”, the group sees a clip of a much younger Cody happily interacting with his uncle Darius Dunn... who in the present has already tried to kill him. As the clip is brief and Dunn seems genuinely happy while playfully ruffling Cody’s hair, it’s completely left to the viewer to wonder if there was a time that Dunn ever had any genuine love for his nephew, or was just being nice in a Pet the Dog moment (which also raises questions if Dunn treats young children any better than, well, literally anybody else).
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    • Did the High Mage genuinely want to help the Underground Mutants and cure their mutations in "Notes from the Underground" part 3, or did he have some ulterior motive? Given that the Underground Mutants are cured only when they are in the High Mage's city, that he wants his race to be reawoken and retake the world it once rulednote  and the fact that he's generally a lying prick, it seems that the latter is true, but it still left to the viewer to decide if he genuinely wanted to help them in some maner or not.
  • Americans Hate Tingle: The series didn't really take off in Japan as well as the 1987 series did; the only seasons dubbed were 1 and 2, after which it was cancelled. This also happened to China, Hong Kong and South Korea itself, which also have only the first two seasons dubbed.
  • Arc Fatigue:
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    • Having an entire six-parter dedicated to a Triceraton invasion of Earth in the "Space Invaders" three-parter followed up by yet another "Worlds Collide" three-parter where the Triceratons invade Earth, leave Earth, come back again, rinse/repeat, and generally go back-and-forth with the Turtles can be quite tedious to sit through. It all depends on whether or not the viewer thinks this long story arc is worth sitting through for the introduction of Agent Bishop and a few other important plot elements in the Triceraton invasion that would be used for later status-quo-changing story arcs such as Ch'rell utilizing Triceraton technology to escape Earth in the later "Exodus" two-parter.
    • The “Search for Splinter” storyline. While the arc itself — by that name — only lasted two episodes, it was interrupted before reaching a conclusion, by the five episode long 'Turtles in Space' arc, finally coming to a close at 'Secret Origins Part 1‘, seven episodes after 'Search' had begun. Putting one story arc on hold for a while will have that effect.
  • Awesome Music: The "Midnight Run" song at the beginning of the City at War trilogy, which expertly captures the light-hearted mood of the brothers enjoying a night on the town while jumping across rooftops.
  • Badass Decay:
    • Bishop appears to suffer from this in Fast Forward, but redeems himself in "Day of Awakening".
    • Both the Justice Force and the Ninja Tribunal suffer from this during the attack on April and Casey's wedding. The Ninja Tribunal are demigods said to be the most powerful Ninjutsu masters on the planet, while the Justice Force consists of several Captain Ersatzes of superheroes like Superman and Green Lantern. Their contribution during this battle consists of being casually swatted aside by the Cyber Shredder and his henchmen.
    • The Demon Shredder is easily the most powerful of the Shredders, or even characters in general, featured in the show, being capable of transforming entire areas to hellish landscapes and summoning legions of undead and demons. His resurrection during the Ninja Tribunal arc was something that inspired fear in even the godly Ninja Tribunal themselves. During his reappearance in Tempus Fugit, he appears to be only as strong as the other Shredders and never utilizes his massive powers.
    • Quarry, Stonebiter and Razorfist are intimidating figures and thoughtful fighters for the first episode of Notes From the Underground and the first few minutes of the second then turn into more passive, easily frightened or defeated characters. This might be justified though given that their leaving their comfort zone to a place that terrifies them, and from what little we see of them in combat against the feral mutants, they are right to be scared since they stand little chance against them.
    • Karai gets a spectacular introduction in season 2, soundly defeating the turtles, taking charge of the Foot Clan, and brokering a peace between the warring factions, all while gaining the turtles' trust. Her later appearances have her demoted to one of Shredder's henchmen who struggles to get even a single victory against even one of the turtles. Thankfully this is undone as she takes a greater role in season 4.
  • Base-Breaking Character:
    • Even to this day, there are fans who loved the twist of making the Oroku Saki Shredder the cover identity of Ch'rell and those who feel the cartoon royally screwed up by radically altering his character; the fact that the show later revealed the Oroku Saki Shredder was very much alive and a real person whose identity Ch'rell stole was likely an Author's Saving Throw in this regard. There's also if he was a cool villain whose Arch-Enemy status to the Turtles was deserved or if he was too overpowered and overly prominent, the latter of which probably isn't helped by a majority of the first three seasons' conflicts eventually revolving around him.
    • Karai herself was also quite divisive of a character. She had her fans who liked her for being a Dark Action Girl who possessed more honorable Hidden Depths. On the other hand, there were also quite a few fans who hated her guts for her going back and forth between siding with the Turtles and being loyal to the Shredder and just wanted her to stop being so wishy-washy and pick a side. After she stabbed Leo (albeit somewhat unintentionally since Ch'rell kicked Leo right into her sword), she became even more polarizing as pretty much all her haters were calling for her head at that point.
  • Big-Lipped Alligator Moment: Several:
    • The fight between the Turtles and the Foot Mystics from "Return to New York" part 2. Up to this point, the Turtles have been facing enemies that are largely Badass Normal (Hun for instance) or at least enhanced in some way (Clothes Make the Superman for the Foot Tech Ninja and Genetic Engineering Is the New Nuke for the Underground Mutants for example). In contrast, the Foot Mystics are explicitly stated to be supernatural. Their weird nature was briefly foreshdowed when April mentioned that the floor they are on wasn't listed anywhere, but it still can be a little jarring to some viewers.
      • Their introduction can come across as this, too. The Turtles enter a weird room with some samurai-looking statues..who inexplicably come to life and proceed to attack them. Compared to other enemies, who appeared in previous episodes (the Foot Tech Ninjas appeared first in "The Way of Invinsibility" and later return in the three-parter), the Foot Mystics never appeared in previous episodes and can feel out-of-place to some.
    • Another BLAM happens in "The Search for Splinter" part 1. Raphael isn't able to find any clues on Splinter's whereabouts, he gets angry and decides to stop some crook he saw. This scene isn't plot-relevant at all and it isn't brought up again.
  • Complete Monster: See here (includes the games).
  • Continuity Lockout: The series didn't adhere to Status Quo Is God, which resulted in a lot of long-running plot threads, major reveals that often end up casually conversed about, and bits of character development from episode to episode that people won't catch unless they watch avidly.
  • Draco in Leather Pants: Agent Bishop gets this treatment from a large portion of the fanbase. While he does change his ways and brings peace and stability to the Earth in Fast Forward, he still committed a lot of evil deeds in the bulk of his appearances, most notably attempting to dissect the Turtles and Splinter multiple times, torturing Leatherhead, ruining the lives of his own men by mutating them into monsters, and torturing countless sentient alien beings in the decades leading up to his ultimate Heel–Face Turn. Even though there's little doubt that Agent Bishop is a complex character and multi-faceted Anti-Villain who himself was experimented on by aliens during the Civil War and thus, has a sympathetic and believable motive for wanting to keep Earth safe from aliens invasions, a lot of his fans still have a tendency to play down all his evil deeds and romanticize him as little more than a noble and selfless Hero Antagonist who only has the best interests of the world at heart, even though many of his pre-Fast Forward actions show that he's NOT(most notably when he openly admitted to Splinter in "Bishop's Gambit" that he honestly doesn't care if innocent people get killed by his Slayers in his quest to root out aliens). What also helps his case is that Bishop tends to be given a free pass by many fans for acts that they would crucify other villains for. When Karai tried to kill the Turtles and Splinter in "Scion of The Shredder" in an assault on their home, fans were about ready to lynch her. However, when Bishop did something similar in "Bishop's Gambit" by forcing the Turtles out of their homes with sonics, kidnapping Splinter, and trying to have the Turtles killed, fan reactions to his ruthless actions were much more muted, if not totally silent, by comparison.
  • Ensemble Dark Horse:
    • Hun and Bishop, to the point of becoming Canon Immigrants.
    • Usagi and Gen are both really popular and tend to steal the show whenever they show up.
    • The Dark Turtles for their cool designs, personalities, and interesting subplot hinting at the start of a redemption arc in their final episode.
    • Viral is quite popular among the artist community, due to her unique design and being the lone villainess in Fast Forward.
    • Chrysalis is probably the most minor member of the Justice Force and never even says a word in the series but is well-remembered by many.
    • Traximus, the triceraton gladiator who becomes Fire-Forged Friends with the heroes and the Rebel Leader against his oppressive government, is seen as a highlight of the three arcs he appears in.
    • Kirby King, the artist whose drawings come to life, is impressively popular for a One-Shot Character. It helps that he's modeled after the late Jack Kirby.
    • Eventual Justice Force member Raptarr is the subject of a decent amount of attention, fan art, and Shipping fics due to his appearance and powers, his Ideal Hero nature, and the interesting Back Story of his species.
    • The Battle Nexus competitor Rings only appears in one episode and is eliminated after a fight that lasts about a minute. Still, his cool use of Deadly Discs and his Barbarian Longhair appearance earn him some fans.
    • In a Meta sense, this version of April is generally better liked than the other versions that aren't Channel 6 reporters.
  • Evil Is Cool:
    • Shredder is The Heavy of the series for a reason. He doesn’t indulge in For the Evulz, he demands proof his enemies perished, and he backs up his bark with an even worse bite every single time he’s in combat. Shredder evolves along with the Turtles to combat them, culminating in his final bid to return to space and conquer and murder untold millions. He does this all despite being a diminutive alien who relies on his mind as much as his robotic suits. It literally took exiling him to a remote ice asteroid in deep space without any technology whatsoever to finally bring him down (and even before that, the Turtles and Splinter resigned themselves to a murder-suicide to take him down).
    • Agent Bishop, the most iconic character created for the series and for good reason. He’s well-regarded for being brilliant, crafty, and genuinely dangerous in direct combat. His interesting backstory made him stand out amongst the series’s villains as well.
    • The Foot Mystics for being personifications of the elements under the Shredder’s control, and for providing one hell of a fight against the Turtles and Splinter. They make a return in Seasons 4 and 5 and prove they were worth their initial hype.
    • The Dark Turtles have intimidating designs and interesting personalities, and prove to be worthy adversaries to their original counterparts in every encounter.
  • Fanon:
    • Some fans have speculated that the villain Khan from the seventh and final season of the show was actually one of the four Foot Elite who were relatively prominent supporting villains from the first five seasons due to sharing the same leitmotif as them.
    • Leonardo is widely believed to be blind in the Bad Future shown in Same As It Never Was, to the point where many assume it's canon, though Word of God says that wasn't the intention (but didn't outright joss it).
  • Fanon Discontinuity: For some fans, Fast Forward and Back to the Sewer seasons. This is because both seasons are lighter in tone and more episodic compared to the prior ones. Fast Forward also drastically changes the premise of the show by transporting the Turtles to the future.
  • Fan-Preferred Couple:
    • April and Donnie receive a lot more attention than April and Casey do.
    • Leonardo and Karai also get this. Despite there not being all that much Ship Tease between the two, a lot of fans prefer to ship the two of them due to their similar sense of honor and personalities.
  • First Installment Wins: A variation. The post-retool seasons, Fast Forward and the Back to the Sewers Soft Reboot aren't as well-regarded as the first five seasons, due to dropping most of the arcs, serialized storytelling, and serious tone that made the earlier seasons so well-liked, and having fairly gimmicky premises that said seasons mostly tried to avoid. Although some of Fast Forward's characters (such as the Dark Turtles and Viral) are well-liked enough that people would love to see them again in a new incarnation.
  • Franchise Original Sin: One of the bigger criticisms of later seasons is the Shredder tends to become the center of the conflict, often to the extent of pushing other, more interesting villains who were driving the plot up to that point out of the spotlight. In spite of this, Season 1 had this issue, with a number of subsections of the Foot Clan showing up, or revealing the villain of the episode had been working for the Shredder, but at that point, the Shredder was the only major antagonist in the series, so it wasn't as much a problem because most of the villains at that point lacked depth.
  • Growing the Beard:
    • While Season 1 is good, Season 2 started putting greater focus on the characterization of the main cast, started to rely much less on the Foot Clan as a major threat in less plot-relevant episodes, and began to weave the story arcs that would come. Season 3 then followed it up with major status quo changes that affected the Earth as a whole, and giving the series more than one central villain, each with their own long-term plan and interesting characterization.
    • Season 4 is usually considered the high point of the series, due to having some complex and surprisingly well written arcs for both Leonardo and Michelangelo and an interesting change to the status quo following the final defeat of Ch'Rell.
  • Harsher in Hindsight:
    • An In-Universe example in Fast Forward. Serling has made a compilation of his home movies with Cody. There's lots of adorable, funny moments like Serling having to change Cody's diapers... and then we see a video of Cody getting patted on the head by a seemingly jolly Uncle Darius, who'd just been outed to him as a villain in the previous episode. The mood gets awkward, and Serling mumbles that he should probably remove that clip.
    • Zog's failed attempt at a Heroic Sacrifice to try to kill the Shredder cemented him as one of the show's most beloved one-off characters and easily makes it one of the series' most tragic moments - and leads to some heartwarming callbacks as Mikey later names two separate Triceratops note  after him in his memory. In the 2012 series, Zog fully regains his bearings, turns on the Turtles, and calls them out for taking advantage of them before dying as a loyal Triceraton soldier. It's arguable that this Zog would've done the same if he had regained his own bearings, making this Zog's sacrifice even more bittersweet.
    • Leonardo accidentally stabs Splinter in his nightmare in “The Darkness Within”. Come “The Ancient One”, he ends up actually injuring Splinter after losing his temper.
  • Heartwarming in Hindsight:
    • In "Hunted," Leatherhead shows deep care for Michelangelo when he accidentally hurts him and is extremely happy when he Michelangelo alive and well. Fast forward to the 2012 series, where the two become best friends.
    • In "Tale Of Master Yoshi," Leo spoke fondly of Tang Shen, since he states Yoshi’s story is about "a girl." Come Teenage Mutant Ninja Turtles (IDW) and you see Shen and Leo being mother and son respectively, especially when the former comforts her older son in spirit.
  • Hilarious in Hindsight:
    • In "Shredder Strikes Back: Part II", Raph flashes back to the Shredder's (first) defeat, and states that "Nothing Human could have survived that!" Much later, it would be revealed that the Shredder isn't human.
    • 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, but even before that, Peter Laird confirmed that the Triceraton Shredder shown in concept art of a possible second Fast Forward season would have been Ch'rell hijacking the body of a Triceraton soldier, and Back To The Sewers not-so-subtly implied in its first episode that Ch'rell would fight the other two Shredders in the show (there would have been an arc called "The Shredder Wars"). Making the claim that Ch'rell would never be seen again hysterical.
    • On a similar note, there's this exchange, from season 5, before the Cyber Shredder was introduced (and, consequentially, before Turtles Forever and the whole 'Multiverse' thing).
      Mikey: 'Real Shredder', 'True Shredder', 'Utrom Shredder'...
      Donnie: How many Shredders are there?
    • Early on in season 1— the episode "The Garbageman"— Mikey tries out several catchphrases, much to his brothers' distaste. One of those catchphrases is "It's trench-coat wearing time!". Nobody (except the fans) seems to have a problem with "It's ninja time" five seasons later.
    • The Dark Turtles from the Fast Forward season have far more distinct designs than the Turtles, with Dark Leonardo having the most balanced physique, Dark Raphael having a bulkier form, Dark Donatello being taller and slimmer, and Dark Michelangelo being somewhat smaller than the rest. Barring Michelangelo, almost all of the design traits are exactly like the 2012 incarnation of the Turtles, who were all made distinct aesthetic-wise. Dark Raphael also has spikes protruding from his body and shell, which also makes him resemble Raphael's mutated pet Turtle Spike, who would become the 2012 incarnation of Slash.
    • "The Return of Nano" has a bit of back and forth on Not a Date between Casey and April. During the climax, Donatello needs April's help for his plan and runs off with her, leading Casey to bemoan "that sneaky, little green nerd" running off with his date. This exchange got funnier in light of the three characters being in a love triangle on the 2012 series.
    • The 1987 series was a Lighter and Softer show that received a retool late in its run that made the last couple of seasons Darker and Edgier. The same thing happened to this show, but in reverse: This was a Darker and Edgier show that received a retool late in its run that made the last couple of seasons Lighter and Softer. Also, both retools wound up being very unpopular with their respective audiences.
    • Leo ends up becoming Bash Brothers with Miyamoto Usagi. Since then, Michael Sinterniklaas has been in several other works where his character's love interest is voiced by Stephanie Sheh, who's well-known for voicing a certain other famous Usagi.
    • Related to that, April gets to meet Usagi in the show's Christmas Episode. Veronica Taylor would later be cast as an ally to that other Usagi as a fellow Sailor Guardian.
    • Michelangelo is voiced here by Wayne Grayson. Later on, the Turtles meet the Dynamic Duo in Batman/Teenage Mutant Ninja Turtles. (granted, the Robin in that series is Damien Wayne, rather than Dick Grayson. Grayson does appear, as Nightwing, in Vol. 2 and as both Robin and later Nightwing in Batman/Teenage Mutant Ninja Turtles Adventures)
    • In the Fast Forward season, one of the Turtles' major enemies is Viral, who in particular is often at odds with Donatello due to his role as The Smart Guy in the group. One year later, Donnie's voice actor plays a completely different character named "Viral" (though pronounced "Vee-ral" in that case).
    • An animated adaptation where a long-running reptilian team is transformed into dragons to tackle a worldwide threat. Are we talking about the "Ninja Tribunal" season or the fourth Sgt. Frog film?
    • Mikey is a superhero fanboy who becomes a superhero himself (specifically a Badass Normal in a show full of powered hero, meets numerous superheroes (including Nobody, who bears a superficial resemblance to Batman), and becomes a reserve member of the Justice Force. Fast forward to the Nikeloden era and the TMNT have crossed over with Batman multiple times.
  • Ink-Stain Adaptation: Karai's characterization in the comic was very different than how she was portrayed in this series, but the latter got so popular this is usually what fans think about when the name of the character comes to mind, and all the other adaptations where she appears took from it in a way. The popular public perception of Karai as a young ninja girl being related to the Shredder with varying degrees of Undying Loyalty towards him began with this show. And while she didn't get romantic with Leonardo, the seeds of them playing the Dating Catwoman game still got planted here as Leo and Karai did go back and forth several times in the platonic sense on just how redeemable she really was, which would only fully bloom during a later series like the 2012 show.
  • Jerkass Woobie:
    • Baxter Stockman in the episode "Insane in the Membrane". Sure, he was an arrogant jerk, but we learn that he used to be a very sweet kid and in the present day breaks down after seeing hallucinations of his dead mother, which is made worse by his regret of never fulfilling his mother's dreams for her son while she was alive. It's especially hard to not feel sorry for him after he ends up dying after his new body completely decays and Bishop resurrects him, denying him a chance at finally dying in peace.
      Stockman: Why couldn’t you finally let me rest in peace? WHY?
    • The con man in the first episode with Nano may have been using the colony of nanotechnology for his own ends, but as the episode goes on, he legitimately begins to care for him as if he was his son and even expresses remorse after Nano was seemingly destroyed and was overjoyed to see it alive and well in its second appearance.
  • Magnificent Bastard: Agent John Bishop is the leader and founder of the Earth Protection Force, an anti-alien task force Bishop designed after undergoing trauma and experimentation at the hands of aliens. Believing that all aliens and mutations are enemies of humanity, Bishop keeps himself alive for centuries to secure humanity's "safety", creating an entire clone army under the U.S. government's nose and even successfully staging an alien invasion to gain more funding for the EPF. Bishop is as dangerous in combat as he is in strategy, as he dances around entire groups of trained combatants including the Turtles, Karai and Hun, always using nothing but his surroundings and quick-thinking to get the upper hand and keep up. By the year 2105, Bishop has come to see the error in his hatred of all aliens, and develops a peace treaty between several alien worlds and Earth, becoming the beloved President of the new galactic federation and keeping the peace with a gentle but firm hand.
  • Memetic Mutation: The fact that Leo rides a scooter and Raph knows how to knit are both still popular jokes among the fandom.
  • Moral Event Horizon: See the right section of this page for the examples.
  • Narm:
    • The family-friendly swearing by having the turtles say "what the shell?" rather than hell can get a little silly sometimes, especially in otherwise serious moments.
    • Season four's "Scion of the Shredder" features Karai responding to the foot soldiers under her command with "excellent" three times in a row in the span of a few minutes. It's easy to be reminded of Mr. Burns from the Simpsons and runs the risk of undermining a very dramatic sequence.
    • Some of the recycled animation can take a viewer out of it at times. For example, the Utroms coming to the rescue in “Exodus, Part 2” is lifted wholesale from “Secret Origins, Part 1”, but with new dialogue dubbed over.
  • No Problem with Licensed Games: The first and second games (Battle Nexus) based on this series have a cult following, the latter especially thanks to its' challenging enemies, lengthy campaign, lots of replay value, tournament mode, and inclusion of the original arcade game. The third game was not quite as well received but still has something of a following.
  • Older Than They Think: As reviled as Fast Forward was, the entire concept of the Turtles being able to walk freely in daylight where humanity has integrated with aliens from outer space does have its Mirage precedence, albeit done differently than in the show. By the time of Volume 4 of the Mirage series which began running in 2001, a full two years before the 2003 show even premiered and a full five years before Fast Forward became a season, the Utroms came to Earth to establish peaceful relations and as a result, humanity sees an influx of aliens integrating into their society. After that, the Turtles are able to walk freely in public under the guise of being aliens.
  • Only the Author Can Save Them Now: Several times, most notably with the resolution to the Demon Shredder arc.
  • Retroactive Recognition: In the Japanese dub, this was one of the earliest jobs Tetsuya Kakihara did as Leonardo, before his Star-Making Role as both Simon and Jin Kisaragi.
  • 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 fact that his existence indirectly leads to the death of Viral is another black mark.
    • Cody and Serling were this to April and Casey.
    • Almost the entire new Rogues Gallery from Fast Forward, with the exceptions of Viral and the Dark Turtles, weren't very well received for replacing the more popular villains like Hun, Bishop, and so forth. The fact that they were more in line with typical Saturday morning cartoon villains sure didn't help, when the show was known for writing more complex and interesting antagonists.
  • The Scrappy:
    • While the “Fast Forward” season was maligned for many reasons, a substantial amount of the blame is still heaped upon Cody Jones, due to how he was basically The Load added to the existing team dynamic of the turtles and Splinter, with most of the Fast Forward episodes based around him being a turtles fanboy and his uncle conspiring against him. He got more competent later in the season, but this lead to people having the opposite complaints- Cody became the one who ended up saving the day more often then not (especially in "Day of Awakening") which got him labelled as a Creator's Pet to some extent.
    • Starlee's family is rather annoying. Her mother is snobby and thinks of her species and planet as above others and acts rather rudely (she thinks Donatello is a criminal for wearing a mask, and asks if he's had his vaccination shots when he knocks everyone down to avoid getting hit by a laser). Her little brother also messes with things he's not supposed to touch and gets away with it apart from Starlee yelling at him. It's not much of a surprise to see why Starlee didn't want everyone to meet her family.
    • The Ninja Tribunal, due to a majority of them being huge assholes who constantly manipulate their disciples.
  • Seasonal Rot:
    • Season 5 is divisive: many people felt it did a good job wrapping up the remaining plot threads from the previous season, while others felt it was overly gimmicky and too much of an anime/Avatar ripoff, abandoning the series' original roots of being influenced primarily by the original Mirage comics. All that being said, Season 5 is still much better received compared to Fast Forward and Back To The Sewers due to having a Darker and Edgier plot in the form of the Demon Shredder, exploring the martial arts lineage of Master Yoshi and The Ancient One in the Ninja Tribunal, maintaining the same level of animation and artwork from the first four seasons, giving final closure to the Master Yoshi subplot, and generally having an epic Series Finale feel to top everything off.
    • The two retools from Seasons 6-7 are where the rot firmly set in for the majority of viewers. They made the show much more child friendly and typical (robots, digital realms, collect the clues saga).
  • Signature Scene:
    • Season 1: From “Return to New York, Part 3”, despite having been decapitated by Leo, the Shredder’s body gets up, picks up his severed head, and walks away just fine.
    • Season 2: The Reveal of the Shredder’s true nature in “Secret Origins, Part 3”, and then the final showdown with Drako and the Ultimate Ninja in “The Big Brawl, Part 4”.
    • Season 3: Bishop handily fighting off the combined forces of Hun, Karai, and the Turtles in “Hun on the Run”, establishing him as a credible third party in the show’s conflict; the climax of “Same As It Never Was” in which the Bad Future counterparts of most of the cast perish (including the Shredder who meets a particularly messy death at Donnie’s hands); and the scene in “Exodus, Part 2” where the Turtles and Splinter agree to perform a Heroic Sacrifice to stop Shredder.
    • Season 4: Leo’s "The Reason You Suck" Speech to his brothers and Casey in “Dragons Rising”; Leo harming Splinter in a fit of rage and later finally making peace in “The Ancient One”; and the cliffhanger ending of “Ninja Tribunal” (which notoriously went unresolved for two real-world years for fans in the U.S.).
    • Season 5: The epic scene where the Turtles lead forth an army of their allies and enemies to attack the Tengu Shredder’s fortress in “Enter the Dragons, Part 1”.
    • Season 6: Darius’s last ditch attempt to kill Cody in “Turtle X-Tinction!” with Serling giving his life (temporarily) to stop him; Dark Leo reflecting on how he’s been changed for the better at the end of “DNA is Thicker Than Water”.
    • Season 7: The “Shredder War” briefly seen in “Tempus Fugit”; the final scene in which Casey and April are married, watched by all the characters of the series.
  • Strangled by the Red String: Downplayed in regards to Chaplin’s attraction to Karai. He bases the Amazon bots after her appearance due to being smitten with her and her fighting capabilities, but the show doesn’t touch on it again until the final episodes of Season 5, when Chaplin refuses to leave Karai behind during the battle... and when Karai takes his hand as they leave the battlefield together. Both characters only make one more appearance in the final episode as guests at Casey and April’s wedding, so it’s left as an ambiguous Maybe Ever After.
  • They Changed It, Now It Sucks!:
    • 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. It was hit with this even more in Japan, where they were more fond of the 1987 Turtles.
    • Shredder being an Utrom caused quite an outrage.
    • One of the reasons Fast Forward is disliked, between the Lighter and Softer tone, more episodic storytelling, and the jarring shift in the show's premise and setting by transporting the turtles to the future.
    • Of the many complaints Back to the Sewers had, one of the biggest was the change in art style compared to the first six seasons. The removal of the turtles' Irisless Eye Mask Of Mystery in particular got more than a few complaints.
  • They Wasted a Perfectly Good Character:
    • Or characters, in this case The Dark Turtles. Mostly due to their subplot being dropped to make way for Back to the Sewers. Dark Leo's time with the turtles in their final appearance suggested the four had a chance to turn good at some point, but this would never come to pass. Details of the cancelled second season/seventh confirms that they would come back and even fight on the turtles' side, becoming the future's version of the turtles eventually, but, since it was cancelled, that never happened and their status is left ambiguous.
    • The Rat King's appearance in "I, Monster" hints he'll reappear, but afterwards only cameos in the finale to Back To The Sewers.
    • Leatherhead just about vanishes from the series after Season 3. He puts in a major appearance for the "Good Genes" two-parter at the end of Season 4, but doesn't return until the final episode of Back to the Sewers. His absence is especially odd during the last episodes of Season 5, in which the Turtles round up all their local allies and enemies for their final battle with the Tengu Shredder.
    • Bishop fails to put in any sort of appearance during the final season bar a quick cameo in literally the final moments of the final episode.
    • T9851 could have made some appearance during the arc of mutations being caused by Bishop to get some closure, but remains absent throughout it and is left as a single-episode "Shaggy Dog" Story.
    • Mr. Touch and Mr. Go might have made nice additions to Hun's revamped Purple Dragons and help transition it for a street gang to something more organized but are never seen again in that seen again. Likewise, it would have been interesting to see the more notable and long-lasting Purple Dragons goons who'd been with Hun for so long transitioning into the roles of more hi-tech, heist oriented criminals throughout those episodes.
    • Given Season 5's connection to feudal Japan, it's kind of a shame that Usagi and Gen never made an appearance in that season.
  • They Wasted a Perfectly Good Plot:
    • In season 3, the Turtles existence is revealed to the world's leaders by the Triceratons when Zanramon displays a captured Donnie to the world. Nothing ever comes of this, though the Earth was rather preoccupied with a hostile alien invasion of the planet and the recovery thereafter. The idea is touched upon again in “Aliens Among Us” when during the President’s press conference, an artist’s impression of what was likely his fearful description of the Turtles is displayed, but nothing comes of this either and it’s played as more of a gag anyway. Neither situation really came off as a public outing of the Turtles like in the spiritual attack in “Bad Day”, so it’s not unreasonable that the show was not changed by either of these events.
    • The Triceratons never appear as a society again after the Season 3 opener. We never see if Traximus’s aim to reform the Republic pay off nor do we hear anything about it until the sixth season, in which its offhandedly mentioned that they’re not what they used to be, implying Traximus ultimately was successful in restoring the honor of his people.
    • Some of the ideas in Back To The Sewers, such as the one-year Time Skip, could have had interesting ramifications if they were properly explored.
    • One of the fantasy warriors from Kirby's world is seen at the Battle Nexus. The show likely was reusing an animation model, but some fans would have liked if he genuinely was from Kirby’s dimension and if this could’ve led Donatello to reconnect with Kirby.
    • To this day, avid fans of the Konami games lament that the series ended and never had the chance to adapt the remaining seasons.
  • Unintentionally Sympathetic: Stockman's constant mutilations by the Shredder. Granted he's an amoral Mad Scientist who clearly would cut open the Turtles if given the chance, but Shredder himself is so, so much worse, and it's hard to see Stockman's punishments as anything else than an act of needless, abominable cruelty by a truly horrific villain.
  • Unintentionally Unsympathetic: As always, Michelangelo is the silly, lovable Plucky Comic Relief, but as his warm, emotional side is far less prominent in this incarnation than in most others, some fans have complained that his Innocently Insensitive moments, while played for laughs, get too frequent, and that he comes across as a bit of a douche because of it. This criticism is not as pronounced as what eventually befell his 2012 counterpart, however.
  • Unpopular Popular Character: To the Turtles, Splinter, Leatherhead, and many protagonists in modern times who know of his existence, Agent Bishop is hated and reviled, and for good reason, based on the number of times he's tortured them, kidnapped them, tried to dissect them, and generally made their lives miserable. Even in Fast Forward when Bishop has finally made the turn from villain to hero and is popular with the general populace, the Turtles still have an abrasive relationship with him at best, with Raphael in particular usually making snide remarks and taking verbal jabs at Bishop. To a lot of fans, however, Agent Bishop is bar none THE best character created for the show and has gone on to become perhaps the most iconic villain of the TMNT franchise not named Shredder. Him being a big enough hit with the fans was such that his character eventually became a Canon Immigrant to the IDW Comics and the 2012 TMNT show.
  • Values Dissonance: Jammerhead refers to the Turtles in "Playtime's Over" as "buggers" - whilst this is no more offensive than 'jerks' or 'boneheads' in America, in the UK this is quite a rude word, and not one you'd expect to hear in a children's show.
  • The Woobie:
    • Nano in its first couple of appearances. To recap, in Nano's first appearance, it's defeated by getting dropped into a vat of molten steel, and survived, only to get broken into pieces when it returned. An AI that's only a child at heart and doesn't fully understand right from wrong gets defeats more painful than what the villains in the series endure. Maybe that's why it got a happy ending after all.
    • Donatello has had to deal with some of the worst experiences over the course of the show. He's been in a Lotus-Eater Machine where he's seen Angel die before his eyes, been transported to a Bad Future, where he sees all of his brothers die before his eyes, and learns that Master Splinter and Casey Jones are already dead, been captured and Mind Raped by the Triceratons, and been infected by a mutant virus that turned him into a mindless savage beast and nearly killed him. All of this to the most peaceable, kindly turtle of the team.
    • Though not popular, Serling is probably one of the biggest woobies. Most, if not all the fans hate him and in-universe, the other characters treat him like a slave sans Splinter and Cody, suffers bad luck which is sometimes caused by his buttmonkey status, while other times, his pain and suffering is deliberately caused by the turtles (i.e. trapping him inside a video game surronded by extra lives that look and act like the turtles). Honestly, it's a miracle he never tried to commit robot suicide.
    • The sheer fact that the writers seem to cause Leonardo the most emotional and physical pain out of any of the protagonists makes him a Woobie in the eyes of some fans. Throughout the course of the entire show he's typically the most likely to suffer a No-Holds-Barred Beatdown, teeter on the brink of death, experience Heroic BSoD and is even acknowledged in one episode by Michelangelo to shoulder the majority of the responsibility so that his brothers are free to be themselves. What's more, his near decline into Knight Templar-hood in Season 4 as he struggled to deal with Post Traumatic Stress Disorder left many fans yearning to just wrap him in a blanket and give him a big hug.
    • Poor Leatherhead! He's been flushed down the toilet when he was barely more than a hatchling, rescued and reared by the Utroms, only to be left behind all alone when they returned to their own world, manipulated and lied to by Baxter Stockman, buried beneath a pile of rubble, tortured by Agent Bishop, which has left him with parts of his personality he must work hard to control, pursued by a crazed hunter, believed he'd badly hurt/killed Michelangelo in a fit of rage. Don't worry: Mikey was fine, which left him consumed with grief and believing he was nothing more than a monster and worthy of death, and finally his good friend Donatello was infected by Bishop's mutant virus and turned into a mindless monster. Leatherhead did eventually help Stockman to develop a cure for the virus in time to save Donny, but he was obviously deeply upset to see Donatello that way, and to be initially unable to help him. He may be one of the biggest and strongest heroes in the show, but it seems like just about every time he appears he's suffering from some kind of mental or physical anguish.
    • The Fugitoid/Professor Honeycutt: really depends on whether you find his personality + voice annoying or endearing.
    • One time character T9581. He started life as a human, got married and had a child, only to be mutated by Bishop into a hideous monster with apparently no way of communicating his feelings or intentions, was locked away in cryogenic stasis only to be freed by the Purple Dragons, who started to attack him, escaped from them only to be attacked by Leo and Casey who mistook him as dangerous, and then was attacked by Bishop and seemingly blown up. Although he escapes, he has no way of returning to his former life or family, and the last shot we see of him is the poor creature clinging to a buoy, gazing sadly at the gazebo where he got married. His whole story is a really tragic Tear Jerker.
  • Woobie Species: The Merpeople spend decades, if not centuries, as a horribly mistreated Slave Race. Then, after escaping and making a new life for themselves, they find themselves becoming a Dying Race due to industrial pollution.
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