Ok, now I have the full story because I have read all of the Maze Runner books.
Thomas was sent to the Glade because of the following story:
Dr Ava Paige had slipped a note in under Teresa's door in the WICKED complex and it had read:
"Come see me immediately after receiving this note"
So she met with Thomas and they went when it was dark. Paige opened the door when they knocked on her room door and she let them inside.
She told them that there are 19 workers inside WICKED in the North wing as I am sure and she has asked Thomas, Teresa, Aris(who came just after Thomas and Teresa) and Rachel (who came with Aris) to kill the infected by a poson Paige had concocted herself and gave the four bags with the mixture in syringes, and they said "better too many than not enough", so Teresa went with a hand gun, both Aris and Rachel took Launchers and Thomas only had a back pack, and they went on the assassination mission.
When they got back and they returned to their normal activities and schedules for each and every day, but Chuck had come onto the scene and Thomas started to become fond of Chuck after finding him in a hallway sitting down crying at night.
Thomas later on when his friends had their memories wiped and Thomas observed them in glade from the Observation Room but he later tells Teresa that Chuck has set him over the edge and he now disbelieves in a 'cure' for the flare.
He felt sorry for his friends in the Glade because Newt tried killing himself and he was furious because WICKED let a kid die in the Glade after being stung by a griever in broad daylight and resolves to rescue his friends from the maze.
Thomas tells Teresa his idea and they go to the meeting called on by (by the way, Thomas and Teresa had built and programmed the maze optical illusions such as the sky and Griever hole) Ava Paige but Thomas is angry at her for using his email as a way of her becoming the Chancellor and she stated that it was effective immediately after the previous Chancellor had deceased.
So Thomas proposes his idea of the four of them being sent into the maze but keeps back the fact that he wants to rescue them, but he claims that they can pass information back from the glade into the Observation in real time and Ava is delighted with this idea, and she later approves it and Teresa and Ava come up with a plan while Thomas does as much research as possible for an advantage over the grievers.
When Thomas is on the day of going into the Glade, Ava gives him a special 'tea' made specially for him and says the SHE gave the workers the Flare because they wanted to stop experimenting after the Maze Trials but she didn't want to and poisoned them and killed them using the kids.
But Thomas had been tricked and he passed out when drinkng the tea and he went for the swipe by force and without being able to do anything.
Read all of the books and you will know what I am saying.