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"And as selfish as it sounds, we need to protect ourselves first"
Not his first time, James Dashner includes an important human nature: survival. Humans tend to care mostly about themselves in the case of a catastrophe first, then, after survival, they start thinking about their loved ones. It is unlikely that we find a person who will sacrifice himself to save a very close person. That doesn't necessarily mean that the person who chose survival doesn't like the other person; it is a human nature that is inevitable.
However, Alec here says to save themselves first not because it is human nature. Alec and Mark are one of the unlikely people who would sacrifice themselves for their close ones. Alec says that to tell Mark that they shouldn't act fast and they should make sure they are safe first from any dangers to be able to save Trina and the others without making all of them in trouble and neither save themselves nor their loved ones
"I may look like I was chewed up and spit out by the meanest beast in the jungle, but I'm not heartless"
Alec describes himself in two words: mean but not heartless. The two words might seem similar but they are certainly not. Alec is mean, meaning that he is tough when it comes to tough times that needs serious people and fast reactions. He is also not heartless, meaning that he is merciful and he respects whoever respects him. He is a very kind man with so many emotions. Combining these two features, Alec has a very strong character that cannot be defeated, or more specific, cannot find its weakness.
"He was scared of being scared"
The narrator is talking about Mike, who suffered a lot since the Sun Flares to stay strong. His main fear was to be scared from what he faced, because if he got scared, he could ruin everything and end up being killed. When he is scared, he makes himself weak, and enemies look for the slightest hint of weakness to attack and guarantee success. All Mike cares about is surviving with his friends, so the last thing he wants to have is weakness and fear.
"He tried to save himself the only way he knows how...honesty"
Again, the narrator speaks Mark's thoughts. When they were attacked by the crazy tribe, they wanted answers or else they will kill Mark and Alec. Mark thought that being honest is the only way to get himself out of trouble. When he lies, he might get himself into much more trouble making things only worse. He could say something wrong that accidentally mentioned something that didn't satisfy the tribe. That way, he couldn't explain himself. Especially that he wasn't involved in anything related to the darts, it was a very good idea that he decided to tell the truth, because he will prove to the tribe that he is innocent and he is somehow related to them because the same thing happened to his tribe.
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I'm not familiar with this novel, but from what I have been able to find the rising action takes place when a Berg (flying machine) shows up with its crew wearing dark green suits and shoots people randomly with darts (the darts knock them...