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"Do you believe the end can justify the means?"
Janson, or Ratman, ask this question when he is asked about the trials. Though many gladers died during the trials, he thinks that it should not be something to take seriously when they find the cure. The question here means that can the end, or the cure, prove that the means, or the trials, were for a good cause, although they caused losses and they tortured the gladers? Generally, this question means that it doesn't matter what you use no matter how illegal or bad this thing is, as long as you get what you want with it, and what you want is a good thing in the end. The end/means is a dilemma which is still debated on today by many people.
"She was a link to his past."
Teresa was linked to Thomas telepathically. However, her presence reminded him with his past. His past could be the time when they were with the original creators and they were from the people who created the trials and were best friends. It could also be when Teresa went with Aris and locked Thomas in the Scorch in a gas chamber. She told him to trust her but betrayed him. Both of his past he did not want to remember, so he was happy when WICKED removed the Swipe from Teresa so they could not talk telepathically anymore, neither with her or Aris.
"He couldn't take anymore betrayal. It hurt too much."
After all he has gone through in the Scorch, Thomas was fed up of betrayal. WICKED has promised him with the cure yet betrayed him and put him into more trials. Teresa has told him to trust her yet she betrayed him and put him in a gas chamber with the help of Aris. All his life was a bunch of lies, and he did not know who to trust and who to believe. When he could not take any more betrayal, he thought that Jorge, Brenda, Minho, and Newt were going to leave him with the pain of the launcher and escape WICKED without him. However, his thoughts were wrong.
"...and living hasn't exactly been so great."
Newt resembles the life of every human being who caught the Flare, or didn't catch it. After knowing that he caught the Flare, what is going to be great in life anymore? Especially that he, or anyone who caught it, knows that he or she is going to become a deadly animal and sooner or later the disease is going to eat his or her brain and die. Even when Newt didn't know he was not immune, he didn't like life anyway with all those trials and torture and friends dying. Even the outside world wasn't great; it was all full of cranks who are waiting for any immune to show up so they can eat him alive.
"Everybody wants to live."
Brenda here states the most important human nature: survival. Every human wants to survive, and most people, even when it comes to their closest people, will leave them behind as long as they survive another day. Especially if it a natural disaster or in the story's case, a highly contagious deadly virus as the Flare, everyone will try to find a safe place to live in without having to interact with people who might be infected, or even worse, might be cranks and eat them alive.
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