WICKED, which is an acronym for World In Catastrophe: Killzone Experiment Department, was set up by the world's remaining governments to provide a cure for the man-made Flare virus. As part of this project, WICKED selects about a hundred young adults, including Thomas, and puts them through a series of tests—which, of course, includes The Maze.
Thomas is subjected to the same degree of control as the other subjects in this gigantic experiment. His memories are wiped and then his brain closely monitored to try and find out why it's been able to fight off the Flare throughout all the various tests. Contrary to what Teresa Agnes and Ava Paige might think, WICKED does not have the best interests of its young subjects at heart; it simply sees them as nothing more than human guinea pigs, whose brains are to be messed around in the hope of solving the problem which the world governments themselves created in the first place.