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The Death Cure,
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Ali
He may have figured that out, but I think a lot of it is because after being in the glade and the scorch, he couldn't see WICKED's side as sensible anymore. WICKED caused/allowed so many people to die in the trials and kept manipulating everyone in the trials (and he didn't like how cranks were just dropped off in the scorch and essentially left to die because WICKED didn't send supplies to help them stay alive after dropping the cranks off). And he didn't see the point of all of his friends' deaths. Thomas knew that WICKED didn't care how many people died in the trials, and he couldn't accept that anymore, even though he knew he had before.
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