* In the recent series, how did Baxter Stockman get his spine back when he was reduced to a brain in a jar?
** Assertiveness training?
** Worm cloning?
** He always had the spine. A better question would be: why did his left eye randomly reappear halfway through "Mission of Gravity?"
* In ''Back To the Sewer'', shouldn't they have instructed Serling not to mention anything about Cody to April or Casey? The whole "don't mess with time" trope?
** The series' time travel has consistently being presented as being of the ''Gargoyles''/ [[YouCantFightFate You can't fight fate]] /StableTimeLoop type, making "don't mess with time" a non-issue.
** Also by that point Casey had pretty much already made up his mind about marrying April and starting a family, he was just waiting for the right moment.
* Did the Ultimate Daimyo and "that Time Lady" get kicked out of {{Canon}} during the Fast Forward season?
** If they showed up, we wouldn't have a good starting premise for Back To The Sewers, though. It's more than likely that they knew about it and just decided not to act. Not every hero/{{Reality Warper}}/{{Time Lord}} is required to act, after all.
* How turtles are able to wear the protective gauntlet that they (and Foot) use with the Tengu sword? The gauntlet is metal and has five fingers, each of which is smaller than turtles' fingers. Plus, all of five fingers are used when a turtle uses it. The hell?
** It's [[AWizardDidIt special ninja training]].
* Okay, in Wedding Bells and Bytes why the heck is the Khan attack even half a problem? Forgiving for a moment Splinter's age and perhaps not being at full strength because of just being reconstituted we know Hisomi is there as well as the Ancient One so we can infer the Ninja Tribunal is back. The Acolytes are there and Usagi. Seriously WTF. We've seen these characters level entire friggin' ARMIES of bodyguards and elite warriors. The Tribunal alone should have been able to blast this problem and the Cyber Shredder to kingdom come. Instead they wreck the place. In the words of the Blockbuster Buster WTFMOFOS?
* In Fast Forward, how the hell did Stockman survive 100 years as an exposed brain?
** Maybe Bishop had Stockman's brain on some preservatives to keep it from decaying.
*** Stockman mentions that he combined what was physically left of him, with some alien DNA left behind when Bishop's lab was destroyed.
* At several points in the series Shredder will list of a series of allieas he has, Ch'rell (his Utrom/birth name,) Oroku Saki, The Shredder and Duke Acureds. We know where most of these came from but where does the Duke Accureds thing come from?
** It is revealed during his trial in the season 3 finale that Shredhead had several other aliases before arriving on Earth. Duke Acureds was one of them.
* In Identity Crisis, the turtles had some memories depicting adventures that never happened such as Leo saving Renet from a saber-tooth tiger, and Raph fighting while dressed as a pirate. What was up with these memories?
** They're simply from adventures never shown in any episodes (much like the famous fake ClipShow from ''Series/{{Community}}'').
* In season 1, the Guardians are always depicted as talking to the Utrom high council who are depicted as three human who speak with one voice (later revealed to be three human robots on top of a tank containing the utroms). Why the human disguise when the guardian obviously knew the truth?
** Just because you know they are doesn't mean you don't get a little grossed out by the looks of them in their true forms no matter how open minded you are, the Guardians as far I could tell from the series ARE human, I could be wrong though.
* In Same as it Never Was, a portion of Leonardo's character design is confusing. Why did he switch his mask out for sunglasses? Was he rendered blind in the past and now relies on his other senses to fight?
** That's the implication, yes.
* In Return to New York - was there ever an explanation given for the mutant Shredders the turtles had to fight? It was assumed they were just really ugly clones of the real thing, but the revelation that the real Shredder is just an alien brain in a suit put the kibosh on that theory. So if the mutant Shredders weren't clones, then what the hell were they? And why did Shredder have them created in the first place?
** They could still be clones only while operating different suits of armor. Or Shredder took some DNA from his human minions, made the clones, and gave them their armor. As for the reason behind their creation, Shredder most likely created them as part of his world domination plans.
** As a theory, perhaps the Shredder was attempting to synthesize
* I've been wondering, where does Casey get his money? He has his own apartment, motorcycle and car, so he has to have some kind of income.
* The Guardians and the Utroms were very quick to chalk off the Shredder as dead when they saw his robot body decapitated. Were the Guardians out of the loop of Shredder being an Utrom as well? Did the Utroms not closely examine the evidence of the Shredder's demise? They'd surely not dismiss simple decapitation as conclusive.
* What is up with the rather wonky age discrepancies of Hun and Casey that we see during Flashback episodes? When we see Hun and Casey together during the flashbacks to when Hun burned Casey's Father's store, Hun looks a lot younger than present day Hun, probably in his late teens. But when Hun appears in the flashback to when Hamato Yoshi dies, he looks the same age as he does in the present, implying that it must have been several years at least since he burned the store. Yet, in the episode where the child turtles try to train Casey Jones, (which is probably several *more* years later) Casey looks about the same age as he did when his father's store burned down. What gives? Either not as much time passed between these events as would at first appear (which means Hun went through a big growth spurt in a short time) or else Casey is a really late bloomer who is older than he looks.
*Actually, when the turtles meet Casey, he's clearly older, most likely a pre-teen/teen. He was very young compared to when he appeared in "The Lesson", so that solves that headscratcher.
* Karai's behavior bothers me. During her debut up until the episode "Hun On The Run" she seemed to be reluctant follower of the Shredder and questioned his methods, but stayed with him because he found her, raised her and taught ninjitsu. Most prominent example of this is in episode "Mission Of Gravity", where she knows that Shredder's method of removing Triceraton engine would kill millions of people and she even told the Turtles that she didn't wish to see so many people suffer because of her father. During the end she said that she could not easily abandon her father, even if he did bad things. Those episodes could make you feel sympathetic to Karai, she knows that Shredder is bad person, but can't simply abandon him, because he gave her home and raised her, after all. Starting with episode "Same As It Never Was" she began to change. In the said episode she, actually her alternate future self, aided Shredder and stayed loyal to him even after he enslaved the entire planet and turned it into living nightmare, with many people either destroyed by him or suffering under his tyrannical rule. Shredder did all those things, yet she did nothing, staying loyal to him, while claiming that she is doing her job. In previous episodes Karai would disobey Shredder and would act against him (most notably in "Mission Of Gravity"), yet here she does nothing, allowing millions of people suffer, something that she could not do in previous episodes. Shredder had crossed the line in that episode, she should have realized that he had gone too far and must be dealt with, yet she remained entirely loyal to him. You could give this a pass, since this was an alternate universe, but that was the sign of Karai's semi-Flanderization which extended to present Karai. During the "Exodus" she was told by Shredder that Utroms had hunted him and were heartless monsters and she didn't knew the truth about her father. But when she finds out why Utroms persecuted her father and learns that he had committed many atrocities, which resulted in deaths of millions, if not more, innocent beings, she doesn't pull a HeelFaceTurn and realize that her father needed to be stopped, instead she seeks revenge against Turtles and is still loyal to her father, even after finding out that he was not as innocent as he told her. By the way, Shredder also tried to kill Karai when she stopped him from killing the Turtles. What is wrong with you, Karai? You learned that your father had caused millions of deaths and suffering throughout galaxy and even attempted to kill you, yet you still think that it is Turtles fault? She only returned to her characterization as reluctant and honorable follower of the Shredder during the TurtlesForever, where she realized that Shredder cares only about his revenge and doesn't listen to her, something she should have realized back in Season 3.
* In Back to the Sewers, where did the second Battle Shell and Turtle Taxi go?
* In "The Freaks Come Out at Night", if the Kanabo virus is vulnerable to Earth's sunlight, why does the mutated pigeon fly around in broad daylight unaffected?
* If O'Neil Tech is contractually forbidden from making weapons, how come Starlee lets the Turtles use the Transendental Lathe to make ninja weapons (and in Mikey's case, a whole suit of battle armor)?
* At the beginning of Season 4, the turtles and Master Splinter are still badly injured from their last fight with the Shredder. Why didn't the Utroms heal them with their advanced technology? Weren't they on good terms with them?