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Thomas is a pretty simple dude. Not quite Forrest Gump simple, but he's about as deep as the shallow end of a swimming pool. The single-mindedness with which he pursues answers about the Glade and its purpose shows that while he wants to know about his surroundings, it's more to alleviate his feelings of disorientation rather than to ponder the bigger questions:
"What's your problem?" Thomas asked, trying to keep the fear out of his voice, trying not to think what the kid had meant by taken. "I don't even know where I am. All I want is some help." (3.42)
At times, Thomas comes off like a whiny little malcontent—especially in the beginning of the book when all he wants is for the other boys to answer his inquiries. Being simple in a complex world is kinda refreshing, though. As readers we always know where we stand with Thomas. His decisions are mostly based on a single driving factor: he wants to figure out the Maze. He wants to be a Runner because it'll help solve the Maze; he wants the girl to wake up and explain things because it'll help solve the Maze; he wants Frypan to make him some gall-dang lunch because it'll help him solve the Maze. You get the idea.
This isn't necessarily a bad trait for our protagonist, though. His purpose in the book is not only to serve as our burgeoning hero, but to be our guide through the world that the author created. What better way to answer the reader's questions than to have a character that has the same questions we want to be answered? (Whoa, how meta… ) By having Thomas slowly discover the new world around him, we are taking that journey alongside him—sharing his confusion, disbelief, and all the other emotions that go along with being dumped into a strange place.
One of the traits that sets Thomas apart from the other boys is his unwillingness to accept the status quo. By the time he arrives, some of them have been in the Glade for two years, so they've developed rules for their society that provide them with structure, safety, and comfort. Most of the boys are content with this. Thomas, however, is never satisfied with the answers he receives and wants to try things out for himself. Like, "Oh, you say that to stay out in the Maze overnight is a certain death sentence? Lemme give that a try."
Combine this with the speed at which he's forced to assimilate into the Glade (and thus unable to slowly gather all of the information that other boys have accumulated over time), and you get a partially informed, extremely curious misfit. When Chuck tells Thomas that he's the talk of the town he's surprised, but it's for good reason:
"Oh gee, let me think. First, you go out in the Maze when you're not supposed to, at night. Then you turn into some kind of freaky jungle dude, climbing vines and tying people up on walls. Next, you become one of the first people ever to survive an entire night outside the Glade, and to top it all off you kill four Grievers. Can't imagine what those shanks are talking about." (23.15)
This works for Thomas, though. By thinking outside the box and not simply accepting what the other boys tell him as truth, Thomas is able to see and do things that the other boys can't because of their complacency. He is the first one to survive a night in the Maze without getting stung, the first one to have the idea of fighting back against the Grievers (which is kinda shocking when you think about it), and the first one to consider following them to see where they go during the day. None of these things would've happened if he was content to just listen to the rules set forth by the Keepers.
In this role, Thomas is able to act as the catalyst. Even though Teresa is officially the catalyst for change—she's the one that shows up and admits she's triggered the end—Thomas is the one who goes rogue and does what he thinks is right, instead of what he thinks the other boys will accept.
The fact that Thomas is branded as an outsider from the beginning makes it easier for him to not follow the rules. Gally hates him right from the get-go, and Alby and Newt just see him as a snot-nosed Newbie who has a lot of annoying questions. Chuck is the only one to befriend him right away, and that's mostly because he's an outcast himself, latching on to the new kid before he can find someone cooler. When Thomas doesn't blindly follow the rules like the other sheep, um, we mean boys, it only further sets him apart. People don't trust what is different, especially when they've worked so hard to make a strange place feel familiar.
Thomas also seeks out solitude. Whenever he's upset or trying to assimilate some new information he runs to the back of the Deadheads. Is he looking for privacy? Peace and quiet? The wardrobe entrance to Narnia? This escape strategy doesn't really endear him to the other boys who prefer to keep a pack mentality, so it alienates him further and breeds distrust from the other kids.
To makes matters worse, kids are always trying to kill Thomas. Ben goes nuts after the Changing and attacks him in the Glade (and earns himself Banishment as a punishment), then Gally threatens to kill him during the Keeper meeting after the "sun" dies. To add insult to injury, when Teresa shows up she keeps mumbling his name. He is constantly being singled out, which makes it hard to lay low or fit in.
There is a method to the madness, however. Whenever you see someone who's always getting picked on through no fault of their own, don't you feel bad for them? Maybe empathize a little bit? That's what the author is doing by making Thomas a pseudo-martyr. We, as readers, want him to come out on top despite being the underdog. We're onto your tricks, Dashner.
Due to the extreme circumstances in which Thomas finds himself, he undergoes significant self-esteem growth over the period of a few days. He starts out as the whining new kid—pouting quite a bit when he doesn't get his way, belligerently disobeying simple orders, and generally throwing a pretty epic pity party for one.
But over the course of the book we notice him getting small wins. After he survives the night in the Maze, he re-enters the Glade feeling like quite the conquering hero… until he notices Gally staring him down:
He almost stopped walking altogether when he spotted Gally up ahead, arms folded and glaring, but he kept moving. It took every ounce of his willpower, but he looked directly into Gally's eyes, never breaking contact. When he got to within five feet, the other boy's stare fell to the ground. It almost disturbed Thomas how good that felt. Almost. (22.48)
As his successes pile up, so does his confidence, which is pretty crucial seeing as he's the one who needs to save the day. By the time he and Teresa figure out that the Maze is actually a code, Thomas has the confidence to assert himself as a leader in order to help everyone escape.