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!!The Books
* AlternateCharacterInterpretation: Is Teresa truly in love with Thomas and [[spoiler: is sorry for what she did in The Scorch? Or is she actually a [[TheSociopath sociopath]] who manipulates Thomas' feelings for her to her advantage? She [[LackOfEmpathy doesn't seem to realize that Thomas would be upset with her actions, opting instead to declare that she's done apologizing and he should get over it.]] It doesn't help matters when she goes over to Thomas acting all cuddly when he obviously wants his space. And also, was her AnguishedDeclarationOfLove genuine, or was it a final mind screw to hurt Thomas since she's dying?]]
* FauxSymbolism: We have a character go through numerous hardships in a world on the breaking point thanks to the actions of those up top having to sacrifice himself to appease the sins of said world. Sound familiar? For added bonus he and the other of the persecuted get to inherit the earth!
* HoYay:
** Throughout the series, it becomes more and more visible for Thomas and Minho.
--> '''Minho (to Thomas)''': If I don't see you on the other side, remember that I love you.
%% ** Alby and Newt. James Dashner has actually teased at them in fan Q&As.
* IdiotPlot: WICKED's plan is basically this: instead of studying the Immunes actual immune system (the part of the body responsible for fighting diseases) they instead focus on mapping their neurological system (that is, the part of the body responsible for making decisions, and feeling emotions, and interpreting data, and making you "you") and never once do they realize that not only are these bodily systems completely unrelated, but that even if they could analyze the human brain to the point where they could copy its layout into another human being, it still wouldn't do anything because the body is dying of a disease, which is why the Immune are immune: their immune system is independent of the brain. WICKED should have studied that much more understood part of the body, but if they had, we would have no plot.
* TheUntwist:
** The "this person we thought was our ally was actually working for WICKED!" plot twist is so overused in the last two books that it's honestly more surprising when someone or something ''doesn't'' turn out to secretly be part of WICKED's machinations.
%% ** The meaning of WICKED. Especially since the first appearance of the full name comes ''directly'' after Thomas brings it up.
* TheWoobie:
** Newt: Hates every living minute inside the Maze. Has the responsibility of leadership weighing on him. Watched his oldest friends die horribly. [[spoiler:Committed suicide but failed. Is infected with the Flare {{for science}}. Has to spend several weeks slowly going crazy before being put out of his misery]].
** Teresa: [[spoiler:Forced to betray her best friend to save their lives. Said friend refused to forgive her for the rest of the series. Tries to save that friend and gets crushed to death just seconds away from safety]].
!!The Films
%% * GermansLoveDavidHasselhoff: Minho's made the film very popular with South Koreans.
* MoralEventHorizon: Gally wanting Thomas to answer for his actions? Acceptable. [[spoiler:Gally wanting to feed him to the Grievers with no way to defend himself? Not so much]].
* WhatAnIdiot: Thomas has just been dumped in the glade and is greeted by its inhabitants.\\
'''You'd Expect:''' This being a song and dance all these characters are well acquainted with, Thomas would be sat down (by force if necessary), then told in detail the exact conditions of his new life. It is in their absolute best interests to make sure every new person that pops up becomes a contributing member of their society after all.\\
'''Instead:''' The characters only give the barest of explanations as to what's going on, pointedly refusing to even ''mention'' the maze, and then they act like it's his fault when he gets curious about it. The only reason they behave this way is because the alternative would have been a clunky exposition dump.