Thomas, we plan on ending the Flare once and for all, and this may come to a shock to you, but you are a munie.
I will never do what you say! I do not need my memories! Sure I used to work for you, but now I know that what you do is wrong!
After the incident with the Glade, I don't want to be controlled by WICKED again.
Hey, we share a common enemy now, so why don't we be friends?
Thomas is held as prisoner in WICKED by Janson to be tested to help make a cure for the Flare, but he hates WICKED and will never do what they say. Plus, he finds out that he's immune to the Flare.
Is Newt there?
Thomas finds Newt, Jorge, Minho, and Brenda, and they break out of WICKED's complex. and they stole a Berg that they used to fly to Denver.
Someone get him off me! Help me!
When they got to Denver, they left Newt in the Berg because he had the Flare, and had to pass tests to enter Denver. After they entered, they received a note from a group called the Right Arm, and the person that sent this was Gally, Thomas's old rival.
No! Leave me alone! I don't need your help!
Newt, come back, we can help you.
After that, they returned back to the Berg to find that Newt was not there, and that he was taken to a town where Cranks (those with Flare) are taken.
No, he's gone!
Then they left to go see Dr. Hans to get rid of the chips in their heads because they were being followed by WICKED. The problem was that Thomas was being controlled by wicked, and tried to kill Hans.
Next, they went to the Crank Palace to find Newt, and Newt told them to back off and leave him alone.