Thomas feels that he has be betrayed by his closest friend, Teresa, after she told him that WICKED is good he truly doubts her loyalty. But now it is not the time to worry about that right now he needs to find an escape to this room in which he is locked up at. After some days it is revealed to him that the world outside is in a post-apocalyptic phase and that a disease called Flare is causing this. It is also revealed that he is immune to the flare though some of his friends are not. After that information he is released and able to reunite with his friends. Apparently all of his friends went through the same although non of them were told about the flare. Eventually the scientist wanted to take the "Swipe" out. The "Swipe" was a device implanted on everyone's brain that made them forget about their past. But something told Thomas that this was a trap, what if WICKED altered somehow the memories and they are not the truth. So Thomas, Newt, and Minho decide not to remove their swipe, for rebelling and not wanting to remove their swipe they are locked at a cell. The next day they are taken by force to the medic center to remove the "Swipe". But luckily Brenda saves them and they manage to get to the hangars where they find Jorge lying on the floor, and he tells them that the rest of Gladers, Teresa and the others, knocked him out and escaped.A quote that I found pretty interesting in the beginning of the book was when Thomas was locked up in the room and the man talks with him and informs him about the situation outside.
"He paused and studied Thomas before continuing. 'Do you think we enjoy all this? You think we enjoy watching you suffer? It's all been for a purpose, and very soon it will make sense to you"
I am not so sure every employee on WICKED agrees to what it is happening in there. But they don't have much of a choice either the world is going through a apocalypsis and a well paying job could come in handy. So I believe that even if the employees are againsts the experimentation going on there, the people outside would be angrier, since they don't grow human for the new experiments, they must take them from the people outside. So I'm guessing if the opportunity is given the people will fight against WICKED and maybe the employees will rebel too.
Another quote I found pretty interesting during the same conversation between Thomas and the Rat Man was when he told Thomas the following:
"Because, Thomas, there's no value on keeping you in the dark," Rat Man said. "Not anymore."So what I am inferring from this is that Thomas used to be one of the most motivated about WICKED maybe that's the reason why they want him to remember about his past so badly, though I doubt that Thomas will believe them even if it was the absolute truth. So maybe the main reason why they want Thomas to have his memories back is because they need him to help develop the blueprints for the cure without hesitation.
I'm really starting to think WICKED is good, despite their horrible measures what else could they do if they want to find the cure for such a lethal disease. I don't really approve to what WICKED has done to those people but.... Desperate times call for desperate measures. So even though the situation is beyond repair WICKED is still trying to do the best to fix it. 