The novel opens by showing Thomas, who is stuck in a padded room and consumed with anger. Not only is he disgusted with WICKED, but he also cannot reconcile the betrayal he feels Teresa has committed back in the Scorch. He can no longer speak to either her or Aris telepathically. Each day, he watches the door, waiting and willing for it to open. On the 26th day, the door opens.

The Rat Man, Janson, announces that does Thomas not have the Flare, as he was previously led to believe. Further, the Rat Man apologizes for all the trials Thomas has had to go through, explaining it was all done so that WICKED could gather data to create a cure for the Flare. Before taking Thomas to his friends, the Rat Man allows him to shower. Thomas feels reborn. He feels human.

Finally, Thomas reunites with his friends. Once together, the Rat Man announces something else: they will get their memories back and have the WICKED tracking devices in their brains removed. Everyone is startled, but that is not all. The Rat Man explains that not all of them are immune. Janson’s list includes Newt. Thomas is flabbergasted.

Thomas, Frypan, Minho, and Newt discuss whether to get their memories back. They agree to refuse the treatment and fight their way out of the compound as soon as they can. Ultimately, Frypan dismays his friends by opting for the procedure anyway. The other three are placed in a room together to think about their decision before yet another test. However, the Rat Man surprises them by announcing they will get their memories back anyway because it will make things easier.

When Thomas is brought into the procedure room, his old friend Brenda helps him break free by injecting one of the guards with a sedative and attacking another. Newt has a slight breakdown and gives Thomas a note to read when the time is right. Eventually, Thomas, Newt, Minho, and Brenda fight their way through the compound to reach the hangar. They learn that their friends have broken free as well but that they left without them. Thomas is devastated, betrayed. Brenda’s friend Jorge flies them to Denver, where they plan to see a surgeon to remove the devices implanted in their heads.

They make it to Denver, where they leave Newt in the Berg to ensure his safety and the safety of the citizens. There, a man approaches them and gives them a note. Thomas immediately knows that it is Gally, the boy from the Glade who killed another Glader and went crazy. Regardless, they meet with him and he explains that the Right Arm is a group with the aim of taking down WICKED.

The group agrees they will join after they get the tracking devices out of their heads. After the procedure, Thomas watches as an infected man is accosted by the guards. The guards themselves are none too pleased with Thomas’s watching, and they take him away with the intent of obtaining a bounty for an immune. Before they can take him away, however, a police robot shoots them, leaving Thomas unscathed. The police robot is controlled by Janson, who tells Thomas to come back for the final testing. He urges him further by pointing out Newt’s worsening condition and explaining that if they can figure out the cure, they can save Newt.

Thomas is again reunited with his friends and they hurry back to the Berg. Inside, they cannot find Newt. Minho discovers a note that explains Newt was taken away to a Crank Palace. The group heads there in search of their friend. Unfortunately, they cannot convince him to come back with them, so they go back to Denver to join the Right Arm. Thomas also reads the note Newt gave him at the beginning of the book. He is startled to find that Newt asked Thomas to kill him. At the airport, they are surrounded by guards in green suits and taken away.

In the place where they are locked up, they find Teresa and some of the others. Fearing that they have been recaptured by WICKED, the group decides to attack the guards. Once the guards are subdued, Thomas interrogates them and discovers that they work for the Right Arm. The Right Arm is gathering immunes in an effort to infiltrate WICKED’s compound. Thomas demands to be brought to the leader of the Right Arm. Because of the danger, the guards suggest that only a couple go. It is revealed that the Cranks are taking over Denver and attacking whomever they come across on the roads.

Brenda joins Thomas and a driver named Lawrence. After a bumpy, dangerous trip that includes some encounters with Cranks, they reach the Right Arm lair. Thomas meets the leader, Vince. Vince explains the plan to infiltrate WICKED by posing as bounty hunters. Once inside, they will plant a device that will render WICKED’s weapons useless, then fight from there. Thomas volunteers to go in ahead of the attack to plant the device, knowing the Rat Man wants him to come back.

Lawrence drives Thomas and a pilot to the airport, yet another dangerous trip. After one near disastrous crash with Cranks, Thomas notices that one of the Cranks is Newt and asks Lawrence to stop the vehicle. Thomas tries to convince Newt to come with them, but Newt is angry that Thomas did not do as he asked in his note. Thomas has a gun and Newt goads him on, trying to get Thomas to kill him. Unexpectedly, Thomas shoots, closes his eyes, and runs back to the van without looking.

It is a sad trip to the forest near the WICKED compound, but Thomas makes it and walks into WICKED, where the Rat Man greets him with open arms. He and two doctors explain that they want to operate on Thomas and perform a live vivisection of his brain. They hope the results will lead to a cure. Thomas tries to refuse and push the procedure off until his friends can arrive, but the Rat Man pushes the procedure forward. Thomas is put to sleep, but wakes up to the alarm sounding and a note from Chancellor Paige directing him to the immunes who are below in the Maze and to a way out of the compound.

Thomas finds his friends and gets them to agree to save the hundreds of immunes in the Maze. Just as they begin to direct people out, the Right Arm begins using explosives on the compound. The walls begin crumbling around them. They hurry to where a portal of sorts awaits them. At the portal, the walls come down in large stones. The Rat Man, along with some guards, stops them. They fight as the walls drop. Thomas and his friends win the battle, which ends with Thomas killing the Rat Man. They head for the portal, but Teresa is smashed beneath the crumbling building. They leave her behind and enter the portal to find a beautiful, green paradise.