After escaping the Maze, Thomas and his peers are sleeping in a dormitory-style setting, having been placed there by their rescuers. Thomas hears a girl speaking to him through his head as he is in bed. For a moment he is afraid that he is in the terrible Box again, the contraption that delivered him to the Maze. He realizes where he is, and realizes that the voice is Teresa again, with whom he shared a telepathic link even before they escaped the Maze. Teresa is separated from the rest of the group, all of whom are teenage boys. After chatting for a bit, Thomas slips back into a dream.
In this dream, a flashback-style story, Thomas is only four or five. He is with his hypothetical parents, who are upset that “they” have “chosen” Thomas. His dream-mother implies that his parents will go insane soon. Suddenly, Teresa tells Thomas that something is wrong. As Thomas tries with difficulty to wake up, he hears screaming. Teresa’s telepathy is suddenly torn from him. The other boys are up and about, and commotion is rampant. A window to the room has been broken, where a bleeding, zombie-like man is standing, his eyes filled with madness. The man says that he is a ‘Crank’, and starts screaming at the boys to kill him. Steel bars still stand in the way between the Crank and the boys.
Minho informs Thomas that these Cranks are everywhere, and that there are no signs of their rescuers. Minho and Newt attempt to open several of the doors that lead out, such as into a common room they had just used the night before, but everything is locked. Finally, using a fire extinguisher, Newt is able to break through a door. Thomas does not feel good about this, but the boys still check out the gloom on the other side. After turning on the lights, they see the dead bodies of their rescuers hanging from the ceiling.
Thomas finds a yellow door from this common room that he thinks leads to Teresa’s sleeping area. He finds a sign on the door that labels Teresa, mysteriously, as ‘The Betrayer’. Breaking in, the boys hear the sound of a toilet and wait for Teresa to come out. However, a boy walks out instead, saying that his name is Aris. Aris also claims to have come from the Maze, or a Maze, but none of the Gladers has ever met him before.
Aris and the Gladers sit down to talk for a bit. Aris has never heard of Teresa. Minho, who left for a bit, comes back to inform them that he has checked out the whole area, and there are no more doors or exits. Thomas checks everything out by himself, lost in confusion, and wonders if their memories have been altered or wiped again. The group talks to Aris and finds out that, like Teresa, Aris had been the ‘Trigger’ in his Maze experiment, and had been the last person and only boy in a group of all girls. Aris also has telepathic speech, and he and Thomas realize they can communicate with each other in this way. They spot a tattoo on Aris’s neck that the boy swears wasn’t there last night. The tattoo says that he is property of WICKED, the larger organization running these experiments, and that he is ‘The Partner’. As they look around, the boys realize that each of them has a label, seemingly designating them various roles. Thomas’s only says ‘To be killed by Group B’.
At this moment a loud bell starts clanging. After it stops, the door to the common room creaks ajar, revealing that the lights have been turned off again. When they go out into the room and turn the lights back on, the hanging corpses are all gone. There is also no more noise of yelling Cranks. The boys discover that brick walls have been erected just outside the iron window bars. The last change is the plaque outside Teresa’s door: where it previously listed Teresa and her designated role, it now has Aris’s label, the same one from his neck. Thomas continues to try to reach Teresa telepathically, and suddenly receives the violent response to telepathic injunction to get out of her head, with Teresa saying that she doesn’t know who Thomas is. Thomas cries into his pillow, and slips into another dream in which people are discussing his potential to save mankind.
Thomas wakes up a few hours later to find everyone still waiting. Several days pass, with everyone slowly starving. There is no food in the facility. In the middle of the third day, a humming noise begins from the common area. Minho wakes up Thomas and gives him an apple. He says that they found apples and something else in the common room. Thomas goes to see for himself what the other thing is. He finds a man in a suit reading a book behind a desk. The man is sitting across the room. Thomas attempts to approach him, but some sort of glass force-field barrier exists. This barrier prevents anyone from reaching the man. It exists, invisible, about ten feet away from the desk.
The man acts annoyed. He says they still have forty-seven minutes left until he is supposed to implement the next part of the Trials. The boys eat and replenish in the meantime. The boys start calling the man ‘Rat Man’ for his rodent-like appearance. Rat Man begins to speak. Thomas catches a suspicious glance between Rat Man and Aris, but is not sure what it means. Rat Man informs the boys that he is a WICKED representative. WICKED is using these mazes and experiments to find a cure for the Flare on behalf of the human race. The human race, inflicted by the Flare, needs to understand certain “killzone patterns” in the brain in order to revive itself. Rat Man says that the Maze was Phase One of the “Trials.” All of the variables thrown at the Gladers were designed to measure brainwave patterns. He says that Phase Two is now beginning, and that it is very difficult. Rat Man tells them about the Flare, which is a disease caused by ravaging sun flares. This disease turns people into the insane Cranks that were trying to hurt the boys earlier. WICKED is an organization working to help cure the Flare. Rat Man says that the boys have all been inflicted with the Flare virus, and to be cured of it, they need to complete the Scorch Trials in two weeks’ time. They are to leave tomorrow.
The boys begin getting ready, packing, and saving food. Thomas is worried about the tattoo branded on his neck about his supposed, upcoming death. Thomas realizes that he no longer knows what is true and what is not. Thoughts of revenge against WICKED comfort him. The next morning, a ‘Flat Trans’ portal-like operation appears on the invisible wall in the common room. The boys walk through.
The first part of the story opens on Teresa conversing with Thomas through their special telepathic link. This sets up her importance to him for the rest of the story. Now that the Gladers are all out of the Maze, it is especially significant that Thomas and Teresa are separated. When Thomas starts to have his flashback-dreams, he remembers that he and Teresa were once very close, and that they also worked closely with WICKED. Suddenly, Teresa screams to Thomas, and then she is taken out of his head. There is no longer any connection there—Thomas “no longer felt that comforting sense of her closeness” (6).
When Thomas and his friends wake up to crazed Cranks outside their windows, Thomas wants to go back to bed, and even thinks about his parents, but acknowledges that “someone had to take charge—they needed a plan if they were going to survive this, too” (8). Already Thomas has started to establish himself as a leader. He is a prominent voice in the group. This is an interesting setup for a leadership dynamic that will play out later in the story, as Thomas and Minho’s leadership styles will complement each other. Either way, Thomas is a natural leader, and a natural planner. He does not immediately act, or act rashly. His first reaction is to ask questions, and feels a “strange calm washing over him” (8).
After Thomas and the Gladers find Aris instead of Teresa, they also find that their necks have been tattooed with labels. Their tattoos not only designate roles for them to play. Their tattoos also bear the label ‘Property of WICKED’. WICKED has been, is, and will continue to treat its subjects just like property. It is almost as though WICKED had forgotten that it is working with real-life, human teenagers, and were instead working with objects.
The Gladers are all slightly unsettled by these tattoos. The tattoos are essentially planned out roles for them to play, whether the subjects like it or not. Newt and Thomas discuss their thoughts about what they are here for, and Thomas says that as long as no Grievers come, he will be happy (45). Newt warns Thomas to be careful what he wishes for—he says, “Maybe they’ll send something worse” (45). While this may be mild foreshadowing of the terrible things that do happen in the tunnel and the Scorch, it is also a twist following up on the first book of the series: instead of WICKED sending things to the subjects this time, WICKED will be sending the subjects out. They will be sending the subjects to the Trials, instead of the other way around.
When the Rat Man finally comes to deliver instructions to the Gladers, he is condescending to them. The boys don’t respond to him, he asks if they are able to understand him. Thomas once notes that the room should have been panicky, but “no one said a word” (60) and Thomas’s own tongue feels dried up in that moment. The Gladers are all so used to being controlled and led around that now, in the face of potential danger and a commanding authority, they can only stay quiet and follow orders.