Brenda reveals that Cranks have broken into the facility before, and Minho conjectures that maybe Cranks have broken in again–tat would explain the alarm and the evidence of weapons leaving the armory very recently. Newt’s temper has been flaring up, and he says that he is already starting to feel not quite right. Newt grabs Thomas aside and gives him an envelope that he says to open at the right time. Thomas, Newt, Brenda, and Minho search for an hour but only find a room with guards tied up and gagged. They leave because they think that it could be a trap. They find their way to a massive hangar; two Bergs are stationed there. A man lying down struggles his way to sitting upright–it is Jorge. Jorge reveals that Teresa and the rest of the subjects found another pilot, overcame the guards, and flew out on a Berg already. They were also the ones who knocked Jorge out just prior to this encounter. Thomas, Newt, and Minho are confused and hurt that Teresa and the other subjects had left them behind intentionally. As Thomas, Newt, Minho, Brenda, and Jorge plan their movements to their own Berg to fly out, a dozen guards rush back into the hangar. Thomas and his friends fire back as they run to the Berg, but both Brenda and Thomas are shot with Launchers before they make it into the Berg. Thomas wakes up from the electrocuting blast some time later.
Brenda and Thomas talk about how the real world is. Brenda tells Thomas that very few places are like the Scorch, which was in the Tropics area. She says that the Berg tracking system knows that Teresa and her crew are headed to Denver. Thomas and Brenda agree that they should go there, too. Brenda says she knows a man there named Hans, who is a doctor. Hans used to work for WICKED before he found their missions and methods too risky, at which point he escaped from them. Hans should be able to take out their implants from WICKED. Thomas finally tells his friends about his dreams, and Brenda tells them thatt she has never been on the side of WICKED. However, their meeting ends poorly when Newt storms out in anger.
When they arrive at the city, Jorge has forged fake documents and gets them all in order. Newt stays on the Berg. The remaining Immune friends arrive in a mall, where a random stranger approaches them and says that he is pretty sure they are the group that escaped from WICKED. He gives them a piece of paper, which has a message saying to meet someone at an address. The message is from a group called the Right Arm; specifically, it is from Gally.
Brenda and Jorge tell Thomas that WICKED orchestrated Gally's murder, along with Chuck’s dive to save Thomas. Gally did not die, as Thomas thought he had. Rather, Gally had gone crazy: he could not handle what he had done. Jorge says that he has heard of the Right Arm, an underground group bent on taking down WICKED. Right Arm is supposedly based here in Denver. Thomas and his friends take a cab out to meet Gally first, on Thomas’s urging. Gally is indeed alive and in Denver, and while he is broken and sad, there is still some bitterness left in Gally’s behavior towards Thomas and Minho. Gally explains that there are two big problems in Denver at the moment. The first is that the Flare has actually broken out, but a corrupt government is doing its best to hide it. The second is that Immune people are disappearing, most probably because WICKED is kidnapping and buying them to do more Trials. Gally had just met with Teresa before this, and most of Gally’s information comes from Teresa, probably because of her memory after the Swipe removal. Gally also tells him that there is a huge bounty out for Hans, because WICKED thinks that Thomas and his friends came to Denver for him–which we know is true.
Thomas and his friends find Hans, who gruffly agrees to help them. As Hans goes into the back room to prep, Thomas suddenly feels WICKED’s control grip his mind. He can no longer control his own body or actions, and grabs a knife to try to stab Hans. They group manages strap him to the bed so the procedure can begin. In his dreams, Thomas remembers that the Purge of the original Creators of the Maze had happened because the Creators contracted the Flare. People like Thomas and Teresa were taken in to replace them. When he wakes up, Hans informs them that he and his wife have to leave for safety reasons. Thomas, Brenda, Minho, and Jorge have coffee in a local shop. An infected man on the Bliss is also in the coffee shop, and is discovered by a Flare-tester. Pandemonium ensues as everyone runs from the shop.
Just before they escape from the WICKED facilities, Brenda reveals that very Gone Cranks have actually broken inside the facilities before. Thomas thinks that very Gone Cranks are “like animals in human form” (68). This thought and Brenda’s words immediately get to Newt, who is stressed about not being immune to the Flare. Newt knows that he is already succumbing to the disease and will eventually become a Crank. This had already changed his mood and approach to life and his friends. While the story is not from Newt’s perspective, even from Thomas’s perspective—the perspective of a close friend—readers are able to observe how the trauma of the Flare’s inevitability affects Newt’s psychology.
When the group of friends runs into Jorge, Thomas is reminded of how he had once been terrified of Jorge, back in the Scorch. That happened before they knew they were on the “same side” (79). Even the way in which Thomas can look at Jorge and think about their past encounters is another indication that the past never goes away: everything from the past still influences everything in Thomas’s present day. In the same way that his flashbacks give him information about the past and provide Thomas with more informed decisions now about how to act, so many other encounters also mark the ways that Thomas’s life has changed over the course of time.
While getting into the Berg, Thomas and Brenda are shot by Launchers, but their friends manage to drag them aboard. Just before Thomas passes out, an “indescribable joy lifted his heart—they were escaping WICKED” (92). Simply the act of leaving WICKED can give Thomas deep joy. The sounds of those words are also very powerful, since WICKED’s name again evokes the idea of “evil.” It is as though Thomas and his friends were finally escaping the source of evil in the world. Thomas can feel this much joy because WICKED appears to be the source of control in his life. He does not have any control over his own life when he is with WICKED. WICKED is like a deterministic weight: leaving them “lifts” his heart.
Later, while talking to Brenda, Thomas thinks about Chuck and why he hates WICKED. He realizes that “Chuck was the most vivid reason that he despised WICKED” (97). The worst part is that he knows that Gally had been controlled by WICKED, too, when he killed Chuck. This makes things even more confusing and perhaps even painful when Thomas and his friends land in Denver and receive a note from Gally. Thomas did not even know that Gally was still alive. He finds out from Brenda, then, that WICKED has also manipulated Chuck. Chuck had not moved in front of Thomas of his own volition: WICKED had moved him. This is another example of WICKED’s extreme control over Thomas’s life, and the lives of all its subjects—and why Thomas hates them so much.
The last surrender of WICKED’s control in Thomas’s body finally comes when he and his friends go to see Hans, the retired WICKED doctor. Thomas nearly stabs the poor doctor with a knife when the doctor tries to remove the WICKED chip. Thomas’s chip has a failsafe which activates when someone is trying to tamper with it. Thomas doesn’t want WICKED to control him, but his body at this time just will not listen. Thomas thinks that it “was such an odd thing to be fighting against something so violently and yet wanting it to happen so completely” (133) when his friends finally strap him down. Ironically, these words could be applied to Thomas’s work for WICKED in general: Thomas very much wants to help humanity at large, but at the same time knows he is hurting himself and others by building the Maze.