I know the creators were controlling
Gally at the end of book when he tried to kill Thomas, but instead killed Chuck. Why did they want Thomas dead?
The creators want Thomas dead because of what he represents. Thomas is destined both save the Gladers and save humanity from the Flare as well. In order to control the action, the creators need Thomas to die.
The Maze Runner
The creators forced Chuck to jump in front of Thomas, as you will learn in the second book. They said it was to "create conflicts in the Killzone". Btw, the killzone is a part of the brain. They never wanted to kill Thomas, because he is too important.
