After a while, as Thomas waits for his friends and the Right Arm to arrive, the doctors come to force him into the procedure. Just then, the alarm goes off–the Right Arm has arrived. Janson still forcibly injects Thomas. Thomas fades to unconsciousness. However, when he wakes up, he is still alive. He finds a letter in the empty room. The letter is from Chancellor Ava Paige, who says that she called off his procedure. She thought that the Trials were over, and that this last step was not necessary. However, her associates disagreed. Her letter includes instructions to take the Immunes with him and go through a Flat Trans to a better place. She has also included a map. Thomas realizes that the Immunes are hidden in the Maze. As he creeps out of the building and sees the hole that the Right Arm’s explosion has caused, he is suddenly caught by Janson and an associate. Janson holds a knife and tries to hurt Thomas, but Thomas overpowers them both. In order to get away, Thomas throws the knife at the associate and kills him. As Janson runs after him, crazed, Thomas realizes that Janson has the Flare–that is why he is so desperate.
Thomas runs into Right Arm associates. The Right Arm members tell him that they are all currently planting explosives to bring down all of WICKED. Thomas realizes that the Right Arm has the darker mission of only destroying the organization, and not taking over. They don’t even care about the Immunes who are still waiting in the Maze. Thomas finds Gally and Vince, and Vince angrily says Thomas will have to hurry if he wants to get the Immunes. Thomas gets Gally on his side. They find Brenda, Minho, Jorge, Teresa, and Aris. Thomas and his friends go back to the Maze. They find hundreds of Immunes in there, which is far more than they expected. They break people into groups of fifty or so, so that a Glader can lead each group to the Flat Trans and safety. While Thomas is instructing the large group, however, the Right Arm’s explosives begin to detonate. A section of the Maze crushes some of the people. Everyone begins to run outwards. A lot of people are crushed in the falling debris and the ensuing stampede. When they exit the Maze, Thomas and Teresa find that, to their horror, Grievers have been activated to kill them. Teresa tells Thomas how to disable them, and he is able to disable most of them. The last Griever, however, comes to life and almost kills Teresa. Finally, she, Thomas, and Minho defeat it. Thomas pushes his way to the front of the group to lead them.
Thomas leads everyone to the maintenance room where the Flat Trans is. He tests it out, and it does indeed work, leading to a green pasture-like place. As he ushers people through the portal, pieces of ceiling and wall are still falling everywhere. Suddenly, Rat Man and seven WICKED personnel show up. The Gladers battle him one last time, and Thomas kills Janson. As Thomas prepares to enter the Flat Trans, a piece of ceiling falls towards him. He stands, paralyzed, watching it. Teresa pushes Thomas out of the way, and the ceiling piece falls on her, crushing and killing her. The rest of the group, including Thomas, runs through the Flat Trans. Brenda disables the Flat Trans from the other side. Teresa’s death pains Thomas greatly, especially because she died saving him.
Brenda burns down the shed that provided the entrance to the Flat Trans. Minho begins directing and organizing the group. Thomas and Brenda relax and watch the sunset. They share a kiss. In a final epilogue, an email from Chancellor Paige to her associates reveals that the Flare was actually purposefully released by the government in the aftermath of the sun flares, as a means of population control. Chancellor Paige says that she had put into motion this backup plan for the Immunes because she was always afraid they would never find the cure, a fear which proved to be well-founded. She hopes that the Immunes can carry on humanity’s existence.
Thomas is again lured into the illusion of choice that the Rat Man puts up again and again. Janson pretends, over and over, to be offering his subjects the choice between doing what they want and what they don’t want, but then takes these choices away at the last minute. Thomas is “frozen” (270) at what is about to happen, again internally chilled, even in a heat-ravaged earth. He has to put all of his hope in the imminent arrival of the Right Arm.
After Chancellor Paige saves Thomas from the surgery, Thomas has to quickly go to the Maze to rescue the rest of the Immunes. He does so with a “sickening dread” (278). This is another indication of the way the past haunts the present. Despite Thomas now knowing the truth about the Maze (that he helped build it) and even having escaped it (and can get in and out easily now), Thomas will never be able to forget his actual experiences from inside the Maze: those will stay with him, and will always make him feel terrible and dreadful about the Maze itself.
When Thomas runs into Gally and Vince, he manages to convince Gally to join his side and stay with the Immunes. This infuriates Vince, who says that Thomas will be a “turncoat” and a “target’ (287). He says that Thomas came in here knowing what their goals were. While this is partially true, Thomas no longer identifies with those goals, and, seeking to finally be under his own control, dares to dissent with Vince. Thomas no longer wants to be under the control of a large organization that dictates what he can or should do.
While Thomas and his friends are in the Maze, the Right Arm sets off explosives that blast pieces of the walls and ceiling onto the people who are still escaping. A piece of rock lands on people, crushing them; everyone watches as “blood oozed out from the edges and pooled on the stone floor” (298). This is reminiscent of the way the Maze Doors closed, in the past. It is also a currently unknown foreshadowing of the way that Teresa will die, for Thomas.
When Thomas and his friends finally reach the Flat Trans, Thomas’s first thought is: “The chancellor had told the truth” (310). Thomas is so used to being lied to that the concept of being told the truth by someone—let alone by the leader of WICKED—is a huge surprise and almost a frightening thing to him. Thomas laughs at this, thinking about how, of all people to help him, the very leader of WICKED has done so; it is so unlike WICKED to tell the truth. Thomas even tests the Flat Trans because he is so suspicious. It is safe, and, like a shepherd, Thomas is finally able to guide the surviving immunes to a paradise.