In Chapter 2, Rat-Man (the guy who told the Gladers about the Scorch Trial at the beginning of the last book) enters the room. Thomas is naturally hostile. There's a bit of verbal back-and-forth, with Thomas being antagonistic and Rat-Man being condescending. At the beginning, Rat Man gets really agitated and angry after Thomas questions his motives (I've included the passage below). Eventually, Rat-Man gets down to business. He tells Thomas that there is "no value in keeping you in the dark... Not anymore." This means that WICKED is going to start revealing important information to him and the Gladers (thank the gods for that). Rat-Man goes on to explain that they almost have all of the data they need in order to produce a cure for the Flare. There are only a few additional things, like fine-tuning that they need. They need the Gladers' input for this. He then tells Thomas that he does, in fact, have the Flare. But, here's the kicker, he is immune to it.