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The book opens with Thomas still in the padded room he was placed in because, according to Teresa, the Flare took hold of him. His own stench bothers him more than the isolation, which he worries is a sign of his impending insanity. He considers the possibility that “Teresa hadn’t been lying after all that last time they’d spoken, when she’d said it was too late for [him] and insisted that he’d succumbed to the Flare rapidly” (11). Nearly overcome with anger, Thomas vows to destroy WICKED, the group that did this to him and his friends.
Each morning after breakfast, he watches the door, waiting and willing for it to open. He spends the time watching the door thinking about his friends. “But most of all, he thought about Teresa. He couldn’t get her out of his head, even though he hated her a little more with every passing moment. Her last words to him had been WICKED is good, and right or wrong, to Thomas she’d come to represent all the terrible things that had happened. Every time he thought of her, rage boiled inside him” (12).
On the 26th day, the door opens.
Through the door walks the Rat Man, the man who had told the Gladers about their last trial. Thomas does not move. The Rat Man sits down at the desk set by the door and opens a folder. He tells Thomas he has plenty of good news and that all the suffering Thomas has been through is for a purpose: “I know we’ve lied to you. Often. We’ve done some awful things to you and your friends. But it was all part of a plan that you not only agreed to, but helped set in place. We’ve had to take it all a little farther than we’d hoped in the beginning—there’s no doubt about that. However, everything has stayed true to the spirit of what the Creators envisioned—what you envisioned in their place after they were…purged” (17).
The Rat Man continues, explaining the importance of reviewing Thomas’ brain patterns to get a sense of what mankind is up against with the Flare. Finally, he tells Thomas that he will remember everything from his past today and, the best news of all, that Thomas is immune to the Flare. Unfortunately for Thomas, the immune are disliked by the people outside.
Reeling from the news that he is immune, Thomas begins to think about why the information the Rat Man has given him must be true. It was “why they’d been chosen for the Trials. Everything done to them—every cruel trick played, every deceit, every monster placed in their paths—it all had been part of an elaborate experiment. And somehow it was leading WICKED to a cure” (21). The Rat Man explains that every action was calculated to help map the killzone of the virus—the brain.
The Rat Man reiterates what WICKED stands for: World in Catastrophe, Killzone Experiment Department. Finally, he takes Thomas to the showers. “Thomas took off his nasty clothes and got to work making himself human again” (24).
“After washing himself from top to bottom at least five times, he felt reborn” (25). Thomas reflects on the past and wonders if things will actually improve from that moment onward. The Rat Man comes to retrieve Thomas and tells him that he will get to see the other Gladers, his companions throughout the past trials. Thomas is relieved when he sees everyone in the auditorium that the Rat Man brings him to. He notices Teresa and approaches her. She tries to grab his hand, which makes Thomas mad. The others take his anger for embarrassment. Thomas distrusts Teresa and wants to make her see that any trust they had before is gone. Before he can speak to anyone else, the Rat Man announces they are removing the Swipe, restoring their memories.
Thomas doesn’t like the idea of remembering: “as it sank in, he realized that something had shifted. Remembering everything didn’t sound good anymore. And his gut confirmed what he’d been feeling since the Rat Man said it was all over—it just seemed too easy” (29). While everyone argues with the Rat Man about whether or not trusting him is a good idea, Teresa speaks out and says, “WICKED is good.” She explains that she cannot think of a better reason why she wrote those words on her arm when she awoke from the coma in the Glade than that it was important for her to remember it.
The Rat Man tells everyone, “If you don’t want to remove the Swipe, don’t do it. You can stand by and watch the others” (31). Thomas contemplates his options; he agrees with Minho and Newt that they will not get their memories back. The Rat Man takes them to a procedure room and explains that giving back memories will also remove WICKED’s control over each of them. Again, the Gladers talk among themselves about whether or not to get their memories returned. Before they can think about it for long, the Rat Man announces something else: some of them are not immune.
The first five chapters introduce Thomas’s new situation—being in WICKED’s compound. Throughout the chapters, we see Thomas develop. From the first chapter, Thomas begins to question his once tight relationship with Teresa and the implications of her final words before their telepathy disappeared. The reader watches as Thomas’s anger at Teresa’s betrayal builds, trapped within both him and the small, padded room. His anger culminates in these chapters with his confrontation with her. Teresa does not know about Thomas’s change in attitude toward her, and when she tries to grab his hand, an affectionate action, he pulls away. His rejection of her signals a reordering of relationships. Teresa is no longer his most trusted friend.
In addition to Thomas’s development, the first five chapters present a clinical theme. Thomas and his friends have been test subjects since the beginning of their trials, but now they are in the compound of those studying them. The first indication of a “clinical” theme comes from Thomas’s own location: a padded room. Similarly, when the Rat Man sits at a desk with a folder of paper, his action hints at a doctor or researcher addressing his patient. He almost mockingly treats Thomas as mentally unstable, suggesting that once Thomas has his memories back, things will be easier because he will be able to think clearly. The Rat Man wears a lab coat and walks Thomas through beige hallways, all culminating in a recurring theme of clinical sterility.
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