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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.
** Newt seems to get fond of Thomas incredibly quickly, shows affection in various ways and shows signs of jealousy repeatedly when Teresa or Brenda are mentioned. Could easily be interpreted as more than simple friendship. It's played up quite a bit in the films, especially when Newt aggressively accuses Thomas of still caring about Teresa. Could be interpreted as just an effect of the Flare, but it could also be jealousy.
** Alby and Newt lead the Glade together and can easily be seen as a couple instead of a regular duo: Newt's hurt reaction when a recovering Alby wants to talk to Thomas only, [[spoiler:the heart-breaking way he strongly reacts when Alby dies]]... James Dashner has actually teased at them in fan Q&As.
* FanPreferredPairing: You'd be hard pressed to find someone who actually ships Brenda with Thomas, as is implied to be canon. Arguably the most popular ship in the fandom is Thomas and Newt (Newtmas), and those who don't ship that usually pair Thomas with either Teresa (Thomesa) or Minho (Thominho).
* 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.
* ParanoiaFuel: The books really push the idea that everything that happens is actually one of WICKED's machinations, making one wonder how one would feel if one's life was also entirely managed by unseen {{Mad Scientist}}s. It doesn't help that, by the end, [[spoiler:everything that happened was pretty much what WICKED, or at least its leader, wanted anyway]].
* SpotlightStealingSquad: If you ask a Maze Runner fan who their favorite character is, 9/10 times they will say [[StoicWoobie Newt]]. Thanks to his [[FountainOfMemes memorable one-liners]], [[BungledSuicide tragic backstory]], and [[TheHeart likable personality]] (the fact that he's played by [[PrettyBoy Thomas Brodie-Sangster]] doesn't hurt either), he has a ton of [[EstrogenBrigade fangirls]], and even critics of the characters have said he was one of the few they liked. [[DeadpanSnarker Minho]] is also one to a lesser extent.
* 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:
* ''YMMV/{{The Maze Runner|2014}}''
* ''YMMV/MazeRunnerTheScorchTrials''
* ''YMMV/MazeRunnerTheDeathCure''

* CompleteMonster: [[DragonInChief Assistant Director Janson]], debuting in [[Film/MazeRunnerTheScorchTrials the second film]], is a cold, self-serving man who serves as the chief operative of WCKD, helping to oversee the Maze experiments with many dozens of children immune to the Flare virus exposed to the horrors of WCKD's Mazes, with countless numbers of them killed. Trying to trick the survivors into letting their organs be harvested under the false pretense of giving them refuge and aiding in an attack on the Right Arm while personally executing Mary, one of their leaders, Janson comes into his own in ''[[Film/MazeRunnerTheDeathCure The Death Cure]]'', where he becomes even more ruthless in trying to procure a cure to the Flare. Janson orders a crowd of protesters fired on by cannons to get at Thomas, smugly implores Thomas to shoot Teresa when he takes her at gunpoint, and having Thomas's friend Minho exposed to [[MindRape horrible, potentially lethal psychological experiments]] to lure him out. Janson ultimately [[spoiler:murders WCKD's head Dr. Paige]] himself and, with the cure revealed to be in Thomas's blood, reveals his true goal to [[AGodAmI build a future of his own design]] by selecting who gets to be cured while leaving all the rest of humanity to be driven insane and slowly die from the Flare. Even in an organization of mad scientists with little regards to [[WellIntentionedExtremist how far they have to plunge to root out a cure to the Flare]], Janson stands out as an utter sociopath with no scruples or benevolent intentions whatsoever.
* TheyWastedAPerfectlyGoodCharacter: In the first two films, Thomas is given the vast majority of the screen time, meaning Newt, Teresa, Minho and other characters don't get near as many memorable scenes as they deserve (and got in the books). This was a problem with fans and critics, especially those who prefer them to Thomas. Luckily, this is amended in the last movie (and in the second movie somewhat for Teresa). Newt gets an emotional and dynamic character arc with his [[spoiler: transformation into a crank]] and some of the best acting in the movie, Minho gets to do more than snark for a change in the scenes where he's being tortured by WCKD, and we get to see Teresa's caring spirit and conflicting emotions as she works to find a cure for the Flare.