In the beginning of this breathless, adventure-crammed tale, Thomas and the Gladers are "safe, rescued, and delivered" to a nice clean dorm, having lived through their escape from the Maze. As Thomas snuggles into his bunk bed, listening to the snores of his friends, he can also hear Teresa speak to him in his mind. Since she is the only girl in the group, their rescuers have sequestered her in a separate room. Speaking mind to mind, they discuss their fear that they will never lose the image of the terrible Grievers. But they haven't seen anything yet… Thomas slips off to sleep and into a dream that seems to be a memory of an event that happened when he was a very small child. In the puzzling dream-memory, his mother cries as she tells her son that she doesn't know why he was chosen, but that he's special. The young dream-Thomas asks if she will become crazy, the way his father and other people have. As the dream ends, he again hears Teresa speaking in his mind: "Tom, something's wrong." That turns out to be quite the understatement. Thomas can't quite seem to wake up, even when he realizes that Teresa is screaming. Even as he sleeps on, he's aware that there are noises around him --- sounds like shrieks of pain, yelling and crashing. But those are nothing compared to his sudden realization that Teresa is gone. Even when he calls her in his mind, there’s no response. Thomas fully awakens…to a living nightmare. The other Gladers are running around pell-mell, staring aghast out the window and obviously terrified beyond belief. He sees a horrifying person standing outside his barred window. The stranger appears crazed --- covered with wounds, scars and burns --- and is begging Thomas to kill him. As if that isn't bad enough, Thomas and the others find an unbelievable sight when they leave their dorm rooms. In the large room hang the dead bodies of their rescuers. As horrendous as things are, Thomas knows he must find Teresa. He goes to the room she slept in, and outside a sign displays these words: Teresa Agnes. Group A, Subject A1. The Betrayer. In the room, instead of Teresa, he finds a boy who introduces himself as Aris. He says he came from the Maze and then proceeds to tell Thomas an incredibly shocking story. Before long, Thomas, along with Aris and the other Gladers, head out on an urgent quest. To reach their goal, they must cross the blazing Scorch. Along the way, Thomas occasionally experiences more of his own lost memories in short-dreamed snatches. Unfortunately, this only makes him even more mystified at what they reveal and what they don't. He also encounters a most unexpected enemy, along with a bit of a romantic triangle, during the ensuing adventure.

After being "saved" from WICKED the Glader's are in for another test called a Trial. They are sent off to a desert and are told to travel 100 miles to the north to reach a Safe Haven with the cure from a horrible disease called the Flare.