This question is in Chapters 1-4. Write in a short answer, not too much detail.
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Thomas' confusion grows because in addition not to understanding where he is, he cannot understand the other boys vocabulary. None-the-less, he doesn't accept his situation, refuses to shake Alby's hand and asks for an explanation. After hearing a scream from outside the walls.... Thomas is further confused and feels as if he's in a nightmare.
The Maze Runner