After being kept in solitary confinement, Thomas is eventually released by Janson (nicknamed the "Rat Man"), who is the assistant director of WICKED (World In Catastrophe Killzone Experiment Department). Janson tells the Gladers (Group A) and Group B that most of their number are immune to the Flare, but some, whose names he reads, are not immune, including Newt. The Gladers are offered the chance to remove the mind-control chips in their heads and restore their memories but at the cost of Thomas's ability to communicate telepathically with Teresa and Aris. Only Thomas, Minho, and Newt choose not to undergo the surgery, as they do not trust WICKED, and Thomas does not want to know who he was when he helped to create the maze. All three of them escape from WICKED with the help of Brenda and Jorge before their chips are removed.
Brenda and Jorge are revealed to be working for WICKED. Thomas initially feels betrayed, but Brenda reveals she only joined so she wouldn't be executed and reasons Teresa may have only betrayed him because of that too. Soon afterward, the Gladers discover that everyone who had undergone the memory restoration abandoned them. Newt gives Thomas a note and tells him to open it "when the time is right." The five then travel to Denver to find Hans, a former WICKED researcher who can remove their mind-control chips. There, a man in a black suit directs them to an address, where Gally is waiting for them. Gally has joined the rebel group the Right Arm and explains that WICKED is capturing every Immune that it can find to prepare another cycle of the Trials. He also reveals that in the decaying cities, many live who suffer from the Flare but take the illicit drug Bliss, which slows down the brain's functioning and helps to relieve the pain that Cranks feel from the Flare.
The group finds Hans, who removes Minho's control chip. However, WICKED uses Thomas's chip to force him to resist the procedure. Brenda, Jorge, and Minho must hold him down so that Hans can perform the surgery. Afterward, the group visits a café, where a security guard apprehends Thomas to sell him to bounty hunters, who will take him to WICKED. Janson intervenes in a holographic, sends a police vehicle to rescue Thomas, and tells him that he must return to WICKED "to save Newt." Thomas and his friends find out in a note that Newt has been taken to the Cranks. Minho convinces them to go to the Denver Crank Palace to rescue Newt, where they bribe the guards to get in. When they meet Newt, he angrily orders them to leave, and the other Cranks chase them out. Thomas then remembers Newt's note, reads it, and discovers that he had begged Thomas to kill him. Thomas despairs over not having read the note earlier.
After returning to Denver, Thomas sees that Newt has succumbed to the Flare. Thomas answers Newt's pleas by shooting him in the head as an act of mercy. The group then discovers that Teresa and the other Immunes have been captured. After knocking out the guards, they discover that the guards were led by Vince, the leader of the Right Arm, who explains that they are infiltrating WICKED's headquarters. Inside, Thomas discovers how Janson tried to use his attempt "to save Newt" to compile data for the cure by examining the physical structure of Thomas's brain, which would kill him. Thomas is forced to begin the deadly brain surgery but manages to plant a device that disables WICKED's weapons, which allows the Right Arm to begin storming the facility.
Thomas wakes up to find a note from Chancellor Ava Paige, the head of WICKED, who explains there are already enough resources from the Trials to make a blueprint for the cure and so his brain is not needed after all. Paige reveals the location of the Immunes "sold" by the Right Arm to gain access to WICKED, and she gives directions to a "safe place" where Thomas should take all of them. Thomas and his friends re-enter the Maze and find the captured Immunes. However, they learn the Right Arm intends to destroy, rather than occupy, WICKED headquarters. Explosions rock the Maze, and falling debris kills some of the Immunes who are inside. Triggered by the commotion, the Grievers come out of storage, but Teresa shows Thomas how to shut them down. Thomas finds a back-door; which turns out to be a Flat Trans. They start herding the Immune kids through the Flat Trans but before Thomas and his friends can escape, Janson and the security guards corner them. They start a fight which ends when Thomas strangles Janson to death. However, Teresa also dies from falling debris to save Thomas's life. Fleeing the building, the Immunes escape through the Flat Trans that leads to a lush paradise. Minho becomes the technical leader, Brenda and Thomas start a relationship and the Immunes resolve to wait until everyone is dead so they can return to the old world.
The epilogue is narrated by Paige. She reveals that after the catastrophic solar flares, the Flare was deliberately created and released by the government as a form of population control. However, the government and WICKED found themselves unable to control the plague. Paige came to realize that they would never be able to find a cure for the Flare and that WICKED's efforts were futile. She realized that the only hope of preventing humanity's extinction was for Immunes to start their society, away from the rest of the world. She devised a plan with Brenda and Jorge to send them to a safe place where they could restore human civilization and so she stated, "WICKED is good."
