Thomas refuses to let Minho die, against Jorge’s wishes. Jorge thinks about his options and decides that he will let Minho live. He will help the eleven boys make it through the city, and will only take one of his Cranks along with him. He comes back out and announces to his fellow Cranks that they will feed the boys. He says that Minho’s punishment will be to have a finger cut off of each hand. Thomas is initially horrified, but something in Jorge’s gaze puts him at ease. Jorge says he will take Brenda with him. Brenda is the other Crank he mentioned earlier, a tough, pretty, older teenager. As they head out without the other Cranks, Brenda keeps Minho at knifepoint in case he tries to charge Jorge. Brenda flirts with Thomas, saying she would have picked him as a leader instead of Minho. She kisses him on the cheek, leaving Thomas feeling emotional and strange.
Jorge and Brenda take the boys into a tunnel where they are fed beans and sausages. Some food production sites specialized in these foods in this area. While they are eating, Brenda explains to Thomas how the sun flares killed a good part of the world’s population. In the ensuing chaos, a virus was released from a disease facility. This virus is the Flare that has infected the Cranks.
Suddenly, there is the noise of an explosion, and a piece of the tunnel ceiling falls down. Brenda grabs Thomas, and they run farther down the tunnel. Thomas sees his friends running in the opposite direction, back up the steps. Thomas and Brenda keep moving farther down the tunnel. When they finally stop, Brenda cuddles against Thomas and makes him promise her that he will take her all the way to WICKED. She says she would rather die than stay in the Scorch area and go insane. She conjectures that Barkley, one of the Cranks in the original group with her and Jorge, caused the explosion. She says that some Cranks like Barkley are farther gone, and probably suspect Jorge and Brenda of wanting to gang up against them. Thomas is uncomfortable with how forward and intimate Brenda is with him, although he has to admit to himself that he does enjoy it to a degree. Thomas insists on going back in the direction they came from, and Brenda proposes that the two of them leave the rest of the group and make it to the cure on their own. When they get to the explosion, they see nobody. They decide to keep going. Brenda says they have to go through the Underneath, a system of underground tunnels. She and Thomas go back into the tunnel.
As they make progress through the tunnels underneath the city, they hear the sound of glass breaking. A group of far-gone Cranks—all with missing noses—appears, and chases Brenda and Thomas through the tunnels. Brenda and Thomas hide in a room off of the tunnels. Just when they think they are safe, one of the far-gone Cranks yanks them out and begins bashing Thomas against the wall. After fighting with him, eventually Thomas and Brenda have to kill him with Brenda’s knife. Thomas is deeply affected by the fact that he just had to kill a man. He refuses to go on further underground. They emerge to the sunlight. They travel until dark, and hide in an abandoned truck in an alleyway. Brenda tells Thomas that WICKED killed her father when they took her away. She also says that she can feel the Flare starting to affect her.
Thomas wakes up from a nightmare. Brenda tells Thomas about a drug called the Bliss, one that Jorge had mentioned earlier. The Bliss numbs Cranks so that the diseased people will not feel the virus as much. When Thomas falls asleep again, he dreams about he and Teresa when they were younger, spying and eavesdropping on WICKED’s plans. The man and woman behind the door are talking about an act of betrayal that comes at the end of the Maze. Presumably, this refers to Gally stabbing Chuck in the first book of the series.
When Thomas wakes up, Brenda is still sleeping. Thomas looks through the windshield and sees a plaque on the alley wall, clearly a sign from WICKED, that says that Thomas is the ‘real leader’. Brenda wakes up and says that these signs are all over the city. That was why she had said she would pick Thomas as the leader, after she found out his name. A little while later, they hear the sounds of a maniacal Crank party going on deeper in the alleyway. They try to leave, but are blocked by a group of three Cranks, all approximately half-gone. The Cranks invite them to their party; when Thomas and Brenda refuse, the Cranks pull out weapons. With a gun pointed at his back, Thomas takes Brenda’s hand and they go down a set of stairs to a door. When they get in there, the man who greets them addresses Thomas by name, saying that they’ve been waiting for him. Down in the party, the man forces Thomas and Brenda to drink a brownish liquid. The liquid is clearly drugged, and soon Thomas and Brenda slip away and are unconscious.
When Thomas and Brenda wake up, the three violent Cranks from the alleyway are surrounding them. They demand to know who Thomas is and why his name is all over the city. One of the Cranks, nicknamed Blondie by Thomas, listens to Thomas tell the full story, and realizes that Thomas is not lying. They are just about to release Thomas and Brenda from their holds when a commotion comes from upstairs. They are afraid that these are full-gone Cranks, but then Minho comes down and frees them. The Gladers and Jorge saw Brenda and Thomas being captured by the Cranks the night before. They are holding the majority of the Cranks hostage upstairs, but Thomas notices that Blondie has gotten away. He is worried about the fact that Blondie has a gun. As the group goes outside, Blondie appears and shoots Thomas in the shoulder with the gun.
Thomas’s mind slips in and out of unconsciousness for several days. Time becomes undeterminable. Jorge removes the bullet, but an infection spreads through Thomas’s body. An aircraft called a ‘Berg’ arrives with WICKED personnel, and takes Thomas on board. He wakes up briefly in some sort of hospital. He hears a man and a woman talking about how they are going to put him right back where they took him from.
Jorge only takes Brenda with him when he joins the Gladers, calling her a “genius” (161) and saying that they need her mind. Thomas soon learns that even amongst Jorge’s group of Cranks there are divisions and factions. The kind of leadership Jorge uses is gruff and mean and pushy. Being a leader, it seems to Thomas, means that one cannot make everyone happy. A Crank named Barkley has mild objections to Jorge’s choice of only taking Brenda. Later, Barkley and some of his friends set up explosives near where Jorge has taken Thomas and his friends.
Brenda is very directly flirty with Thomas. Thomas even comments that “Something wasn’t right with this girl” (175), and says that she is acting a little weird. Thomas is not sure how he feels about this, but he doesn’t completely dislike it, either. Thomas has learned from WICKED—and is still learning—that things are not black and white, especially between people.
Thomas and Brenda have to fight a very crazy Gone Crank in the Underneath, and Thomas is the one to kill him. Brenda keeps telling Thomas that he did the right thing, and Thomas knows that he would have been killed if he had not killed the man first. He also knows that the man was dying anyways and would have rotted away soon. All the same, Thomas really values human life. He is very distraught that he had to take someone’s life, no matter how inhuman they had become (199). This is already a stark difference between him and WICKED, which does not value human life in the same way.
The signs around the city that proclaim Thomas to be the real leader are a reminder of Brenda’s words to him earlier, that he seems like the real leader type. Thomas does not yet have a chance to test out any real leadership abilities before he and Brenda are pulled into a crazy Crank party and made to drink drugged liquids. During this party, Brenda tries to kiss Thomas. To his own surprise, he tells her that she is not ‘her’, with ‘her’ presumably meaning Teresa. Despite Teresa’s strange behavior, Thomas is still very connected to her. This is one example of the way the past always stays with the present. No matter what Teresa has done to him—up until this point—Thomas is still tied strongly and closely to her.
When Thomas is shot by the Crank’s gun right after the party episode, Thomas’s mind is in a haze. Some sort of infection has set in, and everything inside and around him is heat. This is another reflection of the outside world and what has happened to it: like the sun flares that ravaged the earth, Thomas is trapped in a constant cycle of heat, and heated trials.