Thomas awakes in a lift only remembering his name. When the lift halts he is greeted by a group of young boys who also have no memories of their past lives. Thomas discovers he has found himself in the Glade, a small area in which was artificially created by scientists as a testing area. Thomas learns that the Glade is run by a strict order of rules and ideals of hard work. Alby, the leader of the group of boys also known as Gladers, informs Thomas of the maze which lies past the towering walls of the Glade. The maze is a terrifying labyrinth filled with ever changing walls and lethal creatures called Grievers. The Gladers are stuck trying to stay alive as well as "solving" the Maze by running through it as fast as they can while tracking movements of the walls and trying to find an exit. A day after Thomas’ arrival, a girl is brought up in the lift which leaves the boys confused and worried. However, unlike how the other boys arrived, she came up mumbling that everything was going to change and slips into a coma. Thomas seems to recognize her but is unable to pinpoint her familiarity. Wanting to be more than just a mere worker, Thomas decides he wants to become a runner and solve the mysteries of the Maze. Shortly after Thomas is attacked by a boy named Ben who has been stung by a Griever and is going through a phase called the changing. Ben claims he remembers everything and how he knew who Thomas really was. But Alby quickly banishes Ben into the Maze for attempt to murder. While exploring the Maze, Alby was stung by a Griever and another runner, Minho, is unable to drag him back into the Glade before the walls close so in effort to save them Thomas runs into the Maze as the doors to the Glade close behind him, trapping them all in the Maze to survive the night. By miracle. Thomas and Minho are able to hide through the night and bring Alby back into the Glade the next day. Thomas is put into jail for a day for breaking the rules of leaving the glade despite his heroic deeds. After Alby recovers from his Changing process he too recalls Thomas from memories and thinks Thomas had a part in the creation of the Glade and the Maze. Teresa, the girl in a coma, is somehow able to telepathically communicate with Thomas and reveals that they both were involved in the implementation of the Maze. Thomas begins his Runner training under Minho but learns the deep truth of how the Maze has been mapped out completely but has no escape. Later that day Teresa tells Thomas how she has started the end of the Glade. The next day, the sun disappeared and is replaced by a dull grey sky which allows Thomas to realize that the Glade is a fabricated place and that the sky was never real. Teresa informs Thomas that the Maze is a code and he is the key to cracking it. She awakens later that night and meets Thomas in person for the first time. Thomas feels like they share a long history together but can’t remember it. That night the doors to the Maze do not close as they usually do at sundown. Grievers swarm in and attack the Gladers who are virtually helpless unitl sunrise. Thomas determines a new way to analyze the map information. Thomas is able to look at the real maps with Teresa's help. Together, they find a series of letters hidden in the maps, spelling out words. The words have no relation to each other. In order to gain his memory back Thomas decides to get stung by a Griever,
After recovering, Thomas explains that he and Teresa were forced to help the Creators design the Maze. He also knows the way out of the Maze is over a cliff face. The cliff is an illusion to trick them and that it is where the Grievers enter and exit the Maze. If they follow the Grievers down they can find the way out by entering the hidden letter they found among the Maze.
Soon Thomas leads the Gladers into the Maze and they face off against a small army of Grievers. About half of the Gladers die