To tell the whole story from the beginning, WICKED sought out a bunch of immune kids who were supa-smaht, then they found a bunch of smart kids who weren't immune—a.k.a. the control group—and put them all in the Maze.
Ahh, so that explains everything. Still, Thomas is not amused.
Oh, and according to Rat Man, the Variables are all done to stimulate responses in the killzone—otherwise known as the brain—where the Flare does the most damage.
With all of this info now readily available to everyone, let's go follow Thomas.
Rat Man leads Thomas to a room with a bathroom and new clothes and showers and all that jazz.
Finally, Thomas can scrub off that god-awful smell that's been emanating from his body the past few weeks.