Thomas wakes up in a swaying elevator, and the only thing he can remember is his first name. The elevator, called the Box, opens up, and a group of boys lower a rope for Thomas and pull him out. The boys live in a place called the Glade, a courtyard which is surrounded by an enormous labyrinth of 100-foot stone walls called the Maze. Alby, a dark-skinned boy who has been there the longest, is the leader, and his sidekick is a blond boy named Newt. For the past two years, a new boy has appeared in the Box every month. Thomas, confused and upset, demands an explanation about where he is and what’s going on, but when screams sound from a nearby building, the boys leave him with the young, pudgy Chuck, who will become like a brother to Thomas.
The screams are from a boy named Ben; he was stung by a Griever, one of the monsters that lives in the Maze. After receiving an antidote called Grief Serum, Ben is going through “the Changing,” a painful process during which the victim is flooded with memories of his life before the Maze. Gally, a bully who went through the Changing and recovered, confronts Thomas, saying that he saw Thomas during his Changing and doesn’t trust him.
Before dark, four boy run out through four “Doors” in the walls of the Maze, the walls sliding closed behind them. Chuck tells Thomas that these are the Maze Runners, and Thomas feels drawn to become one. The Runners are trying to find a way out of the Maze, and each night, in a concrete room, they map out the eight sections of the Maze. But the internal walls shift every night, creating multiple variations of the Maze, and, so far, they haven’t been able to identify an escape route.
Before dawn the next morning, Newt shows Thomas a Griever through a window in one of the walls. It’s a “horrifying mix of animal and machine,” an enormous monster with metal arms that are capped with saws and shears. Grievers patrol the Maze at night, stinging any boy unlucky enough to be there. Alby explains that the Glade is divided into four areas: the Gardens, where they grow food, the Blood House, where they raise and butcher animals, the Homestead, where they live, and the Deadheads forest, which serves as a graveyard.
An alarm blares out through the Glade, and, for the first time ever, a girl arrives in the Box. She babbles incoherently and then falls into a coma, holding a note reading that reads, “She’s the last one. Ever.” The girl seems familiar to Thomas, but he doesn’t know why. Later, Thomas sees a metal beetle engraved with the word WICKED; the beetle is a spy from the Creators of the Maze. Thomas goes into the Deadheads forest, where he is attacked by a delirious Ben. Before Ben can stab Thomas, Alby shoots an arrow through Ben’s face, wounding but not killing him.
While Thomas is working in the Blood House, he sees an Asian Runner collapse on the lawn. This Runner, Minho, tells Alby and Thomas that he found a dead Griever in the Maze. At dusk, the leaders, called Keepers, bring Ben from prison and push him into the Maze for attempting to murder Thomas. Ben shrieks and howls in terror as the walls close on him.
The next day, Minho and Alby go into the Maze to find the Griever, who, it turns out, was only pretending to be dead. By dinner, they haven’t returned. At the West Door, Thomas sees Minho half-carrying Alby, who has been stung. When Thomas realizes that they won’t make it into the Glade before the Doors close, he jumps into the Maze to help them.
Thomas secures himself and Alby high onto the wall with ivy ropes. A Griever appears, pursues Thomas, and is joined by three Grievers. Using an evasive maneuver, Minho and Thomas trick the Grievers into going off a cliff within the Maze, where they are instantly swallowed up by darkness.
The next day, Alby is still alive on the wall, and he is taken down by other Gladers and given the Grief Serum. The Keepers are divided on what to do about Thomas: he violated the rules by entering the Maze, but he also saved Alby’s life. Minho and Gally fight over Thomas’ fate, and it’s finally decided that Thomas will spend the next day in the Slammer (the Glade’s jail), then join Minho as a Runner.
Word comes that Alby is awake and that he wants to talk to Thomas alone. Alby tells Thomas that during the Changing he learned some disturbing things about Thomas and the girl, and that he knows about “the Flare,” which means nothing to Thomas. Just as Alby is explain further, he starts to strangle himself. After Alby is restrained with Newt’s help, he says that an outside force was in control of his hands. Alby then gives Newt two instructions: “Be careful with the girl,” and “protect the Maps.”
When Thomas visits the girl, she tells him telepathically that her name is Teresa. In her coma, she still has memories and says she and Thomas caused this and were sent to end it. Thomas retreats to sleep in the south corner of the Deadheads.
After his day in jail, Thomas joins Minho. They run through Sections Eight and One of the Maze, then draw maps of those sections and add them to a trunk holding all the other daily maps. The other Runners do the same. That night, Teresa telepathically tells Thomas she has “triggered the Ending.”
The next morning, the boys wake up to find that the sun has disappeared and the Glade is bathed in grey light. More disturbing is the fact that the walls of the Maze are now stuck in the open position, meaning that there’s nothing protecting the Glade from Grievers. Back in the Maze, Thomas and Minho follow a Griever, and when they see it throw itself off the cliff, they realize there’s a hole through which Grievers enter and exit the Maze. Teresa wakes up, and she and Thomas, who have a connection they don’t fully understand, speak to each other telepathically. Teresa is locked in the Slammer, and everyone else prepares for the Grievers to come through the open Maze doors into the Glade.
Barricaded in a Homestead room, Newt, Alby, Minho, and Thomas hear the Grievers approach. Alby, very troubled, runs to the Map room. Gally bursts in and says the Grievers will kill one Glader each night until they’re all dead. As a Griever breaks through the window, Gally throws himself at it. The Griever takes Gally through the West Door and the other Grievers follow.
Alby has burned the Maps, but it turns out that Minho had already moved the real Maps to protect them. Teresa realizes that the Maps are a code, and that by stacking each day’s eight maps together, they can read letters, one letter each day. The Maps spell out six repeating words: FLOAT, CATCH, BLEED, DEATH, STIFF, PUSH. To gain more information, Thomas intentionally gets stung by a Griever, goes through the Changing, and realizes in his visions that the only way to escape the Maze is to jump into the Griever Hole and type in the code words.
After a Gathering, the Keepers agree to the dangerous plan, and about half the Gladers assemble to escape. In the Maze, they’re surrounded by Grievers, but they fight valiantly to make a path for Thomas, Teresa, and Chuck to get to the Cliff. The three make it through the Hole and land in a greasy tunnel. Teresa types the words into a computer while Thomas fights, and kills, a Griever. The last word, PUSH, won’t enter, and Chuck realizes they need to push a button marked “Kill the Maze.”
Thomas, Teresa, and Chuck by the eighteen surviving Gladers, including Newt and Minho, and they go down a winding slide, landing in an enormous lab. Ghostly scientists observe them. A woman enters the room with a boy who reveals himself to be Gally. Gally throws a knife at Thomas, but Chuck steps in to protect him and is killed. As Thomas grieves Chuck, an armed group arrives. They shoot the woman and scientists and lead the Gladers to a bus.
One of the rescuers explains to Thomas that the world was burned up by a series of solar flares and then consumed by a disease they call the Flare. It’s rumored that there’s a cure in the Andes, and WICKED, the Creators’ organization, was testing orphaned children to see if they were tenacious enough to try and recover the cure. The Gladers are taken to a bright dormitory and given pizza, after which they fall asleep.
A memo reveals that the woman in the lab, Ava Paige, was not actually killed, and that the “rescuers” are actually a part of the WICKED plan. WICKED will give the survivors, called Group A, one night’s sleep before sending them on the next part of the experiment. Another group, Group B, is reported to also have performed well.