"Do you believe the end can justify the means?"
The Rat Man, or Assistant Director Janson, asks this question when he is asked about the Trials. Despite the death of so many Gladers and subjects, Janson still believes WICKED is justified in finding the Cure. He asks whether the end, or the cure, can prove that the means, or the Trials, were for a good cause, although they caused losses and they tortured the Gladers. The question, posed rhetorically, suggests 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 that people still debate today.
"She was a link to his past."
Teresa was linked to Thomas telepathically, and her presence reminded him of his past. His past could be the time when they were with the original creators and were best friends with one another. This could also reference the time when Teresa went with Aris and locked Thomas in a gas chamber during the events of The Scorch Trials: she told him to trust her, but then she betrayed him. Both of these "pasts" are times that Thomas does not particularly want to remember, so he is happy when WICKED removed the Swipe from Teresa so he could not talk telepathically with her anymore.
"He couldn't take anymore betrayal. It hurt too much."
After all he has gone through in the Scorch, Thomas is fed up with betrayal. WICKED promised him the cure, yet they betrayed him and put him into more trials. Teresa told Thomas to trust her, yet she betrayed him and put him in a gas chamber with the help of Aris. All his life, Thomas experiences the deep pain of lies and their aftermath, not knowing whom to trust or whom to believe. Thomas thinks that Jorge, Brenda, Minho, and Newt are going to leave him with the pain of the launcher and escape WICKED without him, and this pushes him to the breaking point. He can no longer take the pain of betrayal. Fortunately, however, his fears in this case are unfounded.
"...and living hasn't exactly been so great."
Newt resembles the life of every human being living with the grim reality of the Flare. After learning that he caught the Flare, it is difficult for Newt to see what would make life worthwhile–especially since he knows he is going to become a deadly animal, with the disease eating away at his brain over time. Even before Newt learned that he was not Immune, he hadn't exactly liked his life anyway. With the burden of the Trials and the torture and friends dying, Newt once tried to commit suicide in the Maze–this is the reason for his limp. He hated the outside world, too, which was filled with Gone Cranks. For Newt, living seems to be pain, both before and after he contracted the Flare.
"Everybody wants to live."
Brenda here states the most important human instinct: survival. Every human wants to survive, and most people will leave even their closest friends behind if it means they can survive another day. Especially in the case of a highly contagious deadly virus like 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.
We'll be fine, muchacho. Now that we're here, WICKED will have a hell of a time catching up to us. It's easier than you think to blend in, in a city. Just relax.
Jorge says this to Thomas when Thomas is nervous about arriving in Denver. Thomas has been separated from normal, outside society for so long that he is astonished at the sight of the airport mall. Jorge comforts Thomas, saying that it will be easier for them not to appear suspicious here. While what Jorge says is true in normal circumstances, these words later take on irony when it does become easy for WICKED to find Thomas and his friends. As a matter of fact, it is "harder than Thomas would think" to blend in, especially in Denver, where corruption has attempted to blend Cranks in with the normal population for a long time now.
I didn't know!...How was I supposed know?
Thomas is in a coffee shop when he is unnerved at the sight of an obviously infected man on the other side of the room, clearly drugged up. Soon after, a Flare tester comes in and sadistically hauls away the infected man. In the process, the Flare tester also captures Thomas–he wants to sell Thomas for money. As Thomas watches the Flare tester overpower the drugged Crank, Thomas even feels sympathy for the infected man: although Cranks are dangerous, they were also people once. Thomas prizes the humanity of people, which is why it is so difficult for him to accept WICKED's violence. He hears the infected man crying and shouting that he "didn't know" Bliss was illegal, to which the Flare tester rudely responds that of course the infected man knew that Bliss was illegal. However, the Crank's words are indicative of larger gaps of knowledge: no humans knew the sun flares would happen, and nobody knew that the Flare would be unleashed. Furthermore, nobody knows until the end of this story that the Flare was a secret government operation. Even the perpetrators of the Flare did not know that it would mutate and have these effects.
We've been using our data to select a Final Candidate, and you're the one. We need you, Thomas. It all rests on your shoulders.
Janson attempts to persuade Thomas to come back to WICKED and sacrifice himself for the greater good of science. He uses the weighty language of burden by laying the onus on Thomas's "shoulders." While the 'Final Candidate' business originally sounds unimportant to Thomas, Thomas is later almost swayed to really give himself up, simply because he wants to end all of WICKED's senseless violence. He wants the world to stop suffering, and for there to be peace. However, Janson's words are also not really true: no operation as big as the one he is running could ever really rest just on one person's shoulders. For example, he and his colleagues would have run more Trials if Thomas's operation had been unsuccessful for them.
I don't want any credit.
Thomas tells the Rat Man that he does not want any credit for the things he's done, and for potentially sacrificing himself as the Final Candidate. He says this in response to Janson's offer, in which Janson claimed that WICKED will make sure Thomas gets his credit if he undertakes the final operation. However, even these are tricky and desperate words from Janson: Thomas soon finds out that the Rat Man will try to execute his final operation, no matter what. Furthermore, Thomas may be special right now, but if his operation had occurred and been unsuccessful, there are no guarantees he would have been remembered at all. Death levels everyone, and the world's catastrophes have proved that no one is immune to death in the end. Thomas does not want any credit: all he wants is peace and an end to suffering.
I know the majority of WICKED thought that we needed to get tougher, dig deeper, be more ruthless with our subjects, keep searching for an answer. Begin new rounds of Trials. But what we neglected to see was right before our eyes. The Immune are the only resource left to this world.
In a final word to her associates, Chancellor Paige writes about why she helped Thomas and the Immunes escape. She finally saw clearly that what WICKED was doing was not so much wrong as it was useless. Chancellor Paige still believes that WICKED is good, but she also thinks that their tactics are pointless and wasteful. Sometimes, as the Gladers themselves saw, the real answers are right in front of those looking for them, but those people are blinded to them. For example, Thomas should have realized earlier that the Right Arm was not aligned with his own mission, but it instead took him a long time to realize what was wrong.
