In the dark of an elevator, a teenaged boy awakes with no memories other than that his name is Thomas. When the elevator comes to a halt, the doors open and Thomas finds himself surrounded by around fifty teenaged boys. Their leader, a boy in his late-teens named Alby, welcomes him to the Glade. Surrounded by extremely high stone walls covered in thick ivy, the Glade is a large square piece of land with a few wood and concrete buildings. In each of the surrounding four walls, there is a narrow opening.
Over the course of the next few days, Thomas learns that behind the walls is the Maze – a labyrinthine structure full of Grievers. Grievers are violent mechanical creatures that only come out at night. Since the openings to the Maze, what the Gladers call Doors, close at night, the Grievers cannot get into the Glade. During the day, a few of the boys, the Runners, navigate the Maze in order to find an exit. On the same day every month, the elevator brings a new male arrival. But on the day after Thomas arrives, the elevator returns with a teenaged girl in a coma.
The next day Alby and Minho, a Runner, go into the Maze to investigate a report about a dead Griever. A few minutes before the Doors close, Thomas sees Minho dragging an unconscious Alby towards the Door. With no one else around to help, Thomas enters the Maze right as the Doors close behind him. Inside, Minho tells him that a Griever stung Alby. Thomas and Minho lure a group of Grievers away from Alby and towards the Cliff – a place in the Maze where the path ends and overlooks an empty expanse. As the Grievers charge at them, the boys dive out of the way, causing the Grievers to disappear off the Cliff.
It’s morning and the Doors are open by the time they are able to return to Alby’s location. Newt, Alby’s second-in-command, cures Alby by giving him the Grief Serum, which causes him to go through the Changing. Newt tells Thomas that the Changing is a painful side effect of the Serum that makes people recall some of their memories.
In the following days, the girl, whose name is Teresa, wakes up and tells Thomas that the Maze is code. The sun also suddenly disappears, which causes the Doors to remain open at night. On the first night the doors stay open, the Grievers come into the Glade and carry off a boy named Gally into the Maze. The Gladers hope that the Grievers will only take one boy per night.
The following day, Thomas uses the maps that the Runners made of the Maze to figure out that the Maze’s shifting walls have been spelling out the phrase, “Float. Catch. Bleed. Death. Stiff. Push.” To understand the code’s meaning, Thomas purposefully gets stung by the Grievers so that he can go through the Changing and recover some of his memories. After the Changing, Thomas remembers that to escape the Maze, they must put the code into a computer that is inside an invisible portal. To get to the portal, they must jump off the Cliff.
After convincing them to follow his plan, Thomas helps lead an armed band of Gladers into the Maze. At the Cliff, a group of Grievers are waiting for them. Thinking that they will only kill one person a night, Alby sacrifices himself to the Grievers. But his sacrifice fails and the Gladers must attack the Grievers as Thomas and Teresa make their way into the portal. Inside, Teresa plugs in the code, which shuts down all the Grievers.
The surviving Gladers meet Thomas and Teresa in the portal. They find a slide that brings them to a giant facility where they meet the creators of the Maze. A woman with the word WICKED stitched into her lab coat and a man in a hood approach the Gladers. The woman congratulates them but says there is still one more test. The man takes off his hood, revealing himself as Gally. Seeming to be mind-controlled, Gally throws a knife at Thomas, but a fellow Glader, Chuck, jumps in front of the knife. As Thomas cradles Chuck’s lifeless body, a group of men and women come into the facility and shoot the woman. The Gladers follow them onto a bus and they all drive into the night.
On the bus, the unnamed leader of this group tells the Gladers that in the world outside the Maze, there has been a devastating ecological disaster that has caused a widespread outbreak of disease. WICKED hoped to raise children in the harsh environment of the Maze so that they would be better prepared to face the challenges of the real world. The leader says WICKED’s actions are inhuman and that her group fights to save children from their experiments. They bring the Gladers to a safe-house and give them a place to eat and sleep in peace.
The novel ends with an email by the Chancellor of the Maze Trials, Ava Paige. She writes that the “rescue” was a good finale and that after the group gets a good night’s sleep, phase two of the experiment will begin.