A person wakes up in an elevator with no memory of his past, other than that his name is Thomas. When the elevator doors open, he is pulled into a glade by a group of teenage boys who also have no memories besides what they should be called.
Thomas gradually discovers that the Glade is run by two boys who maintain order by enforcing strict rules. Outside the Glade is the Maze, a labyrinth of high walls covered in ivy that houses strange, lethal creatures known as Grievers. The boys are trying to stay alive as well as "solve" the Maze by running through it as fast as they can while tracking movements of the walls and trying to find an exit to escape.
After Thomas's arrival, a girl is delivered through the elevator into the Glade, and subsequently lapses into a coma. When Thomas comes to visit her, Newt asks him if there is any recognition. Thomas knows that he knew her and is trying to think of her name when a voice inside him starts talking to him as if the girl was saying it: this is how Thomas learns her name. To make matters worse, her arrival triggers everything in the Glade to change: the sun disappears, the deliveries of supplies stop coming, and the doors of the Maze stay open at night, which allows the Grievers to enter the Glade and hunt the children.
Minho, the Keeper of the runners, proposes that the walls of the Maze aren't random, but that their movements are actually a code, leading to the discovery that the Maze is spelling out words. Thomas also discovers that the Cliff that they all thought was just a cliff turns out to be where the Grievers are coming from. If they can come and go over the edge of the Cliff, then maybe so can the boys.
The girl, Teresa, wakes up and tells Thomas that they knew each other before they were put in the Glade, and reveals that they can communicate telepathically.
Most of the Gladers decide to make a run for it, knowing that it could be suicide trying to take on the Grievers, but figuring that nothing could be worse than being stuck in the Glade. They succeed, only to find out that what they've been doing is an experiment being conducted by the Creators, a group called "World In Catastrophe: Killzone Experiment Department" (WICKED). Gally, one of the Gladers who always knew something was different about Thomas and hated him for it, appears at the lab where the teenagers escaped to. He hadn't originally escaped with them, and he is acting strangely, as if he is being controlled. He suddenly throws a knife at Thomas, but Chuck, the youngest Glader and a close friend of Thomas's, throws himself in front of the knife and sacrifices his life. After briefly mourning the death of Chuck, the boys and Teresa are "rescued" by rebels and brought to a safe haven while being told about "the Flare"—an apocalyptic occurrence that killed off half of the world's population.
The epilogue reveals that the "rebel group" may just be another variable in the experiment, and they weren't the only group being evaluated.