Friendship
Friendship is a necessity in the Glade. Without a strong sense of community based on personal relationships, the Gladers would not be able to survive. Relying on one another to fill certain roles allows for a functional society that is self-sustaining.
Thomas is able to make friends after arriving, particularly with Chuck. Chuck believes in Thomas's ability to lead them to safety, but more than anything sees Thomas as his closest friend. Thomas is occasionally annoyed by Chuck, but it is strongly hinted that these boys might be brothers. Thomas also forms a close working bond with Minho. This bond allows Thomas to assume a more active role in the Glader community, and which allows him to lead the others out of the Maze.
Thomas's closest bond, however, is with Teresa. It is a bond that remains largely unexplored by the end of the novel but even the little contact the two characters have with each other is poignant and loaded. They recognize each other as friends even without knowing anything about each other or themselves. Their previous friendship left an imprint that no amount of memory-wiping could fully erase. Furthermore, they each stores some memory of their collective past. In this manner, our friends can be seen as repositories and reflections of our shared lives.
Persistence
Despite having been imprisoned in the Glade for two years, the Gladers have not given up on trying to solve the Maze. Not trying to solve it would mean giving up and succumbing to a sense of hopelessness. Though the task may come to feel pointless, they continue to persevere.
Thomas is able to tap into this spirit when he begins to emerge as a leader. He does this primarily by demonstrating persistence and perseverance when he is trapped in the Maze with Minho and Alby. By not giving up or accepting the traditional viewpoint that a night in the Maze means certain death, Thomas is able to form a plan to keep himself and the other two boys alive. He emerges as a hero who has bucked the trend and given hope to a beleaguered community.
Death
Despite the minor conveniences and comforts the Gladers have managed to establish, the Glade and the surrounding Maze carry a specter of death. Thomas feels this almost immediately upon arriving in the Glade. He only wants to leave and escape. Overcoming this constant sense of fear and trepidation becomes a key point to maintaining his sanity and mental well-being.
Thomas's discovery of the graveyard, and the morbid grave site of the young boy who tried to escape via the Box tunnel, only serve to further cast the environment as one in which life is constantly vulnerable. Awaiting the Gladers outside the protective walls is a world run by monsters where they would likely die violent deaths. The fear of painful and unpleasant deaths, rather than the fear of simply being dead, serves to control the children and limit the chances they are willing to take.
Apocalypse / Environmental Collapse
Though none of the Gladers can remember what happened to them before entering the Glade, clues suggest that a cataclysmic event took place in the recent path. As a result these children have been rounded up for participation in a cruel social experiment to test their will and perseverance, as well as their intelligence and ability to think and act under extreme pressure.
While it is not clearly expressed what exactly took place in the past, the Gladers suspect that the world as we know it no longer exists. As more of them go through the Changing and remember their past lives, this suspicion is confirmed. Alby is so repulsed by his memory of the real world that he has no desire to leave the Glade. When the Gladers do eventually emerge from the Maze, they see the effects of the Flare and the ravaged landscape. This setting, common in science fiction and fantasy, presents a world without order in which conventional ways of life have been all but eradicated. Humanity is reduced a struggle to survive. It functions as a sort of "re-setting" of society and civilization.
Civilization vs. Savagery
The Gladers' treatment of Ben and his sentencing and punishment bring about feelings of intense guilt in Thomas and highlight the savage rule of law that governs the Glade. Thomas does not feel that it is ethical or humane, and that it reflects the mindset of a culture bent on survival by any means necessary.
This savagery is also expressed by the Creators themselves. They have chosen to subject orphans to a horrific experiment, though they believe their intentions to be good. Dashner presents a world in which catastrophic events have driven human beings to resort to their most base and savage instincts. The Creators believe in their efforts despite the obvious toll.
Order vs Chaos
The Gladers rely on order, one of their primary rules, to maintain their way of life. Order gives their lives in the Glade regularity, hope, and purpose. Without it, the crushing reality of their situation would give way to despair and they would give up or turn on each other. Order allows them to maintain a community instead of fighting against one other.
The Maze is chaotic. It changes every night, making it nearly impossible to map and solve. In the Maze there is no mercy and normal rules do no apply. The Grievers have no set of ethics and extreme caution must be employed at all times. Unlike the Glade, it is not a safe place. The Glade is set in stark contrast to the Maze as a place where some form of civilization still exists - perhaps moreso than in the real world.
Bravery
At numerous times in the novel, Thomas must call on his own will and fortitude to overcome a frightening situation. When he sees Minho and Alby struggling to return to the Glade before the Wall closes, he rushes out to help them. After that, it is his quick thinking and unwillingness to give up that saves his own life as well as Alby's.
These actions also invite prosecution from the Keepers, who feel Thomas has broken the law and must face punishment. Thomas's greatest threat to the order of the Glade is that he questions many of the assumptions on which the Gladers have based their lives. His willingness to face questioning and persecution also requires bravery. Without the will to take risks, no progress is possible. This bravery eventually allows Thomas to show the Gladers a way out of the Maze and on to the next stage of the experiment.
