In the prologue, WICKED soldiers arrive and try to take Newt's sister, Lizzy. However, Newt and Lizzy's parents put up a fight and, as a result, are killed. Since Newt is now an orphan, they take him along with Lizzy as a control subject.
Main plot
In the narrative present, the readers are introduced to Stephen, who has been renamed Thomasby the people in the organization called WICKED. Thomas is only five years old, and since his father has a bad infection of the Flare, his mother has given him up for his safety. He is under the care of WICKED in their main complex in the middle of an Alaskan forest. He meets Teresa, who like him is kept separate from the others. He has to go through blood tests and advanced classes and soon meets Dr. Paige, who acts as a parent to him, and he soon becomes her favorite. They start sneaking out and meet Newt, Minho, and Alby. Newt reveals that his sister had been renamed Sonya and is part of Group B. They start exploring the complex everyday. The trio take Thomas and Teresa into the outside world, only to be caught by WICKED security officers and thrown into the "Crank pits", where they encounter the founder of WICKED, who is nearly past his sanity and writes on a chalkboard that "WICKED is good". The five children are deeply changed by the experience. They don't have any of their secret meetings in the maintenance room for a while, but then Teresa manages to hack WICKED's security systems and allow the friends to meet. Teresa, Thomas, Aris, and Rachel are then recruited to build the Maze. At one of their meetings, Thomas and Teresa stumble upon Charles, nicknamed Chuck, who becomes the little brother that they never had. Their secret meetings continue, with Chuck included. The day after, WICKED finds out that Minho tried to escape, and in front of Thomas they unleash a Griever on Minho, to show him that anyone who tries to escape and gets caught will be harshly punished. After the horrible experience, Thomas goes back and directs all his attention to building the Maze. Shortly after, the Maze is complete, which means his best and only friends are going to be sent into the maze first. Right before they are sent in, Thomas and Teresa go to say their goodbyes. Their friends interrogate them, asking why only they themselves are going in, but not Thomas and Teresa. Not being able to answer truthfully about the Maze being his project only makes Thomas' friends more suspicious, and eventually angry. Chuck does not go with the first batch, and for a long time he, Thomas, and Teresa remain friends. Thomas begins to watch his friends covertly through the "Beetle blades", and sees one of the boys, George, suddenly go crazy and try to kill his friends, only to be killed by Alby. Dr. Ava Paige explains what happened to George, revealing that the Grievers have a virus similar to the Flare and places the cure for it among the Box of supplies, although the cure is at its early stages. A WICKED official named Randall is found outside the complex, infected with the Flare. Dr. Paige then summons Teresa and Thomas and reveals that she suspects some other people at WICKED have the Flare, and sends Thomas, Teresa, Aris, and Rachel to kill those infected, a secret operation that Dr. Paige calls "the Purge". Before the operation begins, Thomas is somewhat reluctant, so Teresa reminds him of her past life she once mentioned. It is then revealed that Teresa was the young girl named "Deedee" who survived in the prequel book The Kill Order. A few months after "the Purge", Thomas is sent to a desert called "the Scorch" to test a Flat Trans and is introduced to Jorge and Brenda, who indirectly reveal that the Gladers will have to go through the Scorch as Phase Two of the Trials. Thomas has come to believe that a cure will never be possible, and as a result, feels that his friends are suffering unnecessarily and vows to save them. Once back at base, Thomas hatches a thorough plan to escape WICKED, beginning with an idea to insert the elite candidates into the Maze with their memories intact, so that they can rescue the Gladers, but Teresa seems reluctant. Teresa takes care of suggesting this plan to Dr. Paige without telling her their true motives. Dr. Paige approves of their plan and the night before his insertion, 24 hours before Teresa's insertion, they spend the night in Thomas's room, somewhat confessing feelings for one another and falling asleep in each other's arms. As he prepares to be sent into the Glade, Dr. Paige gives Thomas a strange type of tea which turns out to be anesthetics. She explains to Thomas that it was her idea to infect WICKED staff with the Flare, because they wanted to end experimenting after the Maze Trials and she did not. She then orders Thomas' memories to be wiped, contrary to their prior agreement. Thomas believes that Dr. Paige has betrayed him and Teresa. Thomas's emotions are then shown as he sees his memories being lost. The book ends with him standing up in the Box, memories gone, setting the events of the main series in motion. Another letter from Teresa shows that she knew Thomas' memories would be erased before insertion, and that hers would not. The letter ends with Teresa stating that she believed in WICKED and would enter the Maze with the words "WICKED is good" tattooed on her arm. She said she believed that one day her friends would thank her.
