WICKED had done all this to him. WICKED had taken his life and those of his friends and were using them for whatever purposes they deemed necessary. (1.10)
Need a reminder that WICKED is a manipulative organization? Well, Thomas reminds us all the time that they're the reasons why his life stinks.
Could it be that the very name they'd used for their organization had been one of the Variables from the beginning? A word with obvious menace, yet an entity they were told was good? (7.2)
An interesting thing to think about: the word "wicked" means "evil." So, on the surface, WICKED would pretty much seem to be evil. But maybe that's a trick, and as some of the kids eventually realize, WICKED may actually be good. Oooh, ooh, but maybe that's what WICKED wants the kids to think. Ugh, now that's how you mess with someone's brain.
"But the worst part is over. We can't change the past, can't take back what has happened to you and your friends. But wouldn't it be a waste to not complete the blueprint at this point?" (10.8)
Promising the kids that "the worst part is over" is another way that WICKED manipulates them. They promise them things that aren't really going to come true, or they tell half-truths, which we all know are lies.
"I was a kid. They brainwashed me into doing those things—into helping." (11.15)
Thomas was manipulated as a kid into helping WICKED design the trials; he realizes this when he has his memory-dreams. In reality, WICKED has been using Thomas's adolescence as a way to brainwash him.
"I bet this is another one of their bloody tests!" Newt yelled. "All of this is meant to happen and we're being analyzed all over again." (14.13)
Exactly. How do the kids know when they're being tested and when they're actually out of WICKED's reach? For all Thomas knows, escaping WICKED and going to Denver is part of the Trials.
They'd been reduced once again to mice, scuttling about in a different kind of maze. (14.37)
Did you get that reference from Book One? We hope you did. The Gladers are all figuratively mice being put through a maze experiment. Well, that's a pleasant and uplifting thought.
"They used him to kill Chuck because the Psychs thought the patterns would be valuable. It was all planned. They forced Chuck to move in front of you." (24.5)
Because WICKED manipulated Gally, they were able to get patterns from his brain processes. But what does Gally get in return? A life of sadness and pain. Sounds legit.
"They swear it's the truth, but they've manipulated and lied so much, it's become impossible to know what's real and what's not real." (51.11)
Just as Newt hints when they're all escaping, it really is impossible to know what's real and what isn't. So even when our heroes get to paradise, is it real? Ugh, maybe we're supposed to find out in the prequel?
Played to the end, Thomas thought bitterly. His own attempts to rebel had turned out to be exactly what they wanted. (58.26)
Despite the whole escaping-WICKED's-headquarters episode, Thomas still proves that WICKED has full control over him for most of the Trials. They actually wanted him to rebel, because that would reveal him to be the Final Candidate.
"The whole world's on the verge of collapse, and you can help save it." (58.30)
This spiel is something WICKED uses to manipulate Thomas and the other Gladers into thinking that sacrificing themselves for the good of the world is worth it. You'll be a hero, they say. But really, the whole hero speech thing, like so much else in this world, is totally meaningless.