Thomas wakes up in a metal elevator that brings him to the Glade. He has no memory of who he is or how he got there, except for his name. He gradually discovers that the Glade is run by two boys: Alby, the leader, and Newt, the second-in-charge, who maintain order by enforcing simple but effective rules. The elevator box surfaces from under the ground once every week and brings supplies of food, tools, clothes, medicine, and sometimes weapons. Every month, a new boy with no memory of anything but his first name also appears in the box.
The Glade is enclosed by a square of concrete walls several hundred feet high. The walls have openings in them, which slide shut every night. Outside the walls is the Maze, a labyrinth of high concrete walls covered in ivy that changes every night. The Maze houses strange, lethal creatures known as Grievers. All that is known about Grievers is that they are a combination of metal and flesh. The Gladers try to stay alive as well as "solve" the Maze by appointing "Runners" to run through it as fast as they can while they track movements of the walls and try to find an exit to escape.
One day after Thomas' arrival, a girl, Teresa, is delivered through the elevator into the Glade. She is the first girl to arrive into the Glade and has a note clutched in her hand that says, "She's the last one. Ever." She says Thomas' name when she's in a week long coma. Later that day a boy named Ben, who was stung by a Griever and went through the "Changing," tries to kill Thomas. Alby saves Thomas and Ben is banished that night.
Minho, the Keeper of the Runners, goes into the Maze with Alby to see what they think is the first dead Griever. Alby is stung by the creature, which causes him to attack Minho who knocks Alby out. Minho carries Alby back to the glade but, by the time they arrive, the doors to the Glade are already closing. Thomas runs into the maze to help with no hesitation, becoming stranded with Minho and Alby. When they hear the sounds of Grievers approaching, Minho runs away while Thomas uses the ivy to pull Alby up the wall. Thomas does his best to survive and keep Alby alive, and by morning Thomas and Minho have killed four of the Grievers.
After returning to the Glade the next morning, Newt calls a Gathering of the Keepers to discuss what to do with Thomas. Some of the Keepers vote to relieve him of punishment, but others, especially Gally, vote to lock him up as a punishment. Minho, however, nominates Thomas to become the Keeper of the Runners, to which Gally disagrees. Gally and Minho threaten each other, and the discussion ends with Gally storming off. Newt, as interim head of the Gathering due to Alby going through the Changing, proposes sending Thomas to the Slammer (their version of a prison) for a day, and then having him start training to become a Runner. Without an official vote, the Keepers decide to go with Newt's plan.
Alby asks to see Thomas alone, without Newt, and tries to tell him something he has seen during the Changing that had to do with Thomas. Before he can give Thomas any real information, Alby starts trying to choke himself. With Newt's help, Thomas manages to stop him. Alby then says it "wasn't really him" and that someone was controlling his actions.
Teresa wakes from her coma, and tells Thomas telepathically that she triggered the Ending. The food is running low, the sky is permanently gray, the box is not coming up, and that same night the maze doors stay open. Alby decides that, to be useful, he'll go into the Map Room and analyze the maps to see if he can find any patterns. Gally comes back that night, and says that the Grievers will come every night now, killing them all off one by one. When the Grievers enter the Homestead, where the Gladers had all been hiding, Gally throws himself at them and they leave.
The next morning, they find out that Alby, weighed down by the reality of the world outside the Maze, had burned all the Maps, effectively destroying any possibility of finding a clue. Thomas later discovers that Minho and Newt actually secured the Maps in the Weapons Room a couple hours earlier, saving the Maps from Alby. Thomas then gets the idea to compare each Map to the Maps of other sections as opposed to other days, and, after copying a couple maps onto wax paper and layering them by day, they find that the first combination spells FLOATCAT. After a couple days of copying maps and layering them, they find that the complete code spelled out by the Maze is: "FLOAT CATCH BLEED DEATH STIFF PUSH".
During the following nights, the Grievers come back, and, as Gally had said, they only take one Glader a night.
Realizing that they won't get anywhere without him getting his memories back, Thomas voluntarily gets stung by a Griever and spends a couple days unconscious as he goes through the Changing to get his memories back. When he wakes up, he knows they have to go down the Griever Hole to escape the Maze, and insert the code into a machine they will find. He also remembers part of the world they came from, knowing a bit about WICKED (World in Catastrophe: Killzone Experiment Department) and his participation in the creation of the Maze.
Using this new information, most of the Gladers leave to try and jump down the Griever Hole. Almost half of them die in the fight against the Grievers, but Thomas and Teresa manage to insert the code, with last-minute help from Chuck to realize that "PUSH" meant to push a button, and it was not the last word of the code.
After exploring the facility they are now in, the remaining Gladers find themselves in a room with scientists watching them. One of them walks out, Gally walking with her. He throws a knife at Thomas, but Chuck dives in, saving Thomas' life though he loses his own.
A rescue team come crashing in a couple seconds later, killing all the scientists that were watching the Gladers, and taking them with them to another facility where they have dinner and go to sleep, sure that they are safe now.
The epilogue is written in the voice of Chancellor Ava Paige, a feature of all the trilogy's novels. She reveals that the group that rescued the Gladers is just another variable in the experiment and that the Gladers were not the only group being evaluated. She reveals that the next day, the second phase of their trials will begin. This leads directly into the events of the next book.
