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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.
** 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.
* 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]].
* 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
* ''Maze Runner: The Death Cure'':
** TearJerker: [[https://www.instagram.com/p/BRUD5fEF1Hs/ This Instagram post, by author James Dashner, of most of the cast at a restaurant before filming resumed.]] The saddening thing is not the idea of them celebrating during [[GrandFinale the final]] ''Maze Runner'' film, it's the first part of the caption that was added along with the image, combining CringeComedy and {{Foreshadowing}} for book fans towards one of the most saddening moments of ''The Death Cure'': [[spoiler:Newt's pleading, final words for Thomas to MercyKill him, as the former has become a Crank. Thomas eventually does it with great remorse afterwards]].
-->''"[[spoiler:[[BaitAndSwitch Please, Tommy, please.... pass the salt]]]]. Good to see these guys back together!!!"''