Thomas wakes up in a box with no memory of his past, other than his name. When the elevator doors open, he is pulled into a glade by a group of teenage boys who also have no memories besides their name.
Thomas gradually discovers that the Glade is run by two boys. Alby and Newt, who both maintain order. Outside the Glade is the Maze, a labyrinth of high walls covered in ivy that houses strange, lethal creatures known as Grievers. Grievers are described as monsters of metal and flesh and are depicted in the film directed by Wes Ball as robotic spiders designed by the organization WICKED. The Gladers 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.Every month the box is sent up with a new person called a "greenie" and every two weeks supplies are sent.
After Thomas' arrival, a girl is delivered through the elevator into the Glade and subsequently lapses into a coma. When Thomas comes to visit her, he recognizes her, but can't remember her name until he hears her voice telepathically in his head. 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. She also arrives with a note from WICKED (World In Catastrophe: Killzone Experiment Department), the creators of the Glade, that says: "She is the last one. Ever." It implies that there were to be no more children sent into the Glade.
Thomas 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 where the Grievers leave the Maze. If they can come and go over the edge of the Cliff, then maybe so can the boys and the girl. This drives Thomas to think they need memories to get out, so he purposefully gets stung by a Griever so he can go through the changing. The changing is a process that begins after you get the serum to cure the infection from the Grievers.
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 the exit, 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 Experimental Department" (WICKED). Gally, one of the Gladers who always knew something was different about Thomas and hated him for it, appears at the lab to which the teenagers escape. He hadn't originally escaped with them, and he is acting as though he is being controlled. He moves to shoot a gun at Thomas, but Chuck, the youngest Glader and Thomas' friend, jumps in front of the bullet.
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 that the Gladers weren't the only group being evaluated.