Thomas wakes up in a dark elevator — 'the Box' — with no memories except his first name. He arrives in the Glade and is immediately surrounded by a crowd of teenage boys.

Alby gives Thomas the standard tour. Thomas sees the Maze for the first time, learns the basic rules, and spends his first night in the Deadheads — the graveyard section of the Glade — unable to sleep.

Newt, the blond second-in-command, befriends Thomas and explains the Glade's social structure more fully. Thomas begins to settle in but is overwhelmed by a compulsive need to run the Maze.

Thomas spends his second full day in the Glade doing menial work, growing increasingly frustrated. He watches the Runners sprint into the Maze at dawn and cannot understand why no one treats escape as an emergency.

Thomas hears the Grievers for the first time from inside the Glade as night falls. Newt explains what they are and what happens if someone gets stung. The fear of the Maze becomes visceral and real.

Thomas is attacked in the Deadheads by Ben, a boy who went through the Changing and is raving that Thomas is responsible for everything. Alby banishes Ben into the Maze at night — a death sentence.

During a run with Alby, a Griever attacks. Alby is stung. Thomas, watching from outside the closing Doors, runs into the Maze to save Alby — breaking the most fundamental rule — and must survive the night inside.

Thomas survives the night and emerges from the Maze to mixed reactions. Alby, badly stung, begins the Changing. The Gathering is convened to decide Thomas's fate — and votes to make him a Runner.

A girl arrives in the Box — the first girl ever — unconscious, with a note saying 'She's the last one. Ever.' Thomas recognizes her without knowing why. She whispers his name before losing consciousness.

Thomas begins official Runner training under Minho. They spend their first full day together in the Maze mapping sections. Thomas notices patterns the others have missed and begins to suspect the maze is solvable.

Thomas and Minho discover a dead Griever in the maze — the first anyone has ever seen. They retrieve a device from its body before it disappears. Alby emerges from the Changing — traumatized, warning Thomas that his memories are dangerous.

Teresa awakens from her coma. She and Thomas discover they can communicate telepathically — a connection that predates the Glade. Teresa tells Thomas she triggered the Ending and that everything is about to change.

The sun disappears — the sky above the Glade goes permanently grey. The Doors stop closing at night for the first time in two years. Grievers begin taking one boy per night.

Gally — a boy who went through the Changing and harbors violent hostility toward Thomas — begins organizing a faction that blames Thomas for the Ending. The community splinters. Thomas considers a desperate plan.

Thomas makes the desperate decision to let himself be stung by a Griever so he can undergo the Changing and recover his own memories. He survives the sting and the agonizing Changing. He wakes knowing the truth.

Thomas presents the escape plan to the Gladers: they will arm themselves and run to the Griever Hole at the far end of the Maze, fight through the Grievers, and enter the exit code on the computer inside. Some will die. They go anyway.

The escape group runs through the Maze at night, battling Grievers with improvised weapons. Several Gladers are killed. They fight their way to the Griever Hole.

Thomas and the survivors enter the Griever Hole, find the computer terminal, and type in the code. The Maze shuts down. They escape through a long corridor into WICKED's underground lab — but at the exit, Gally appears and throws a knife at Thomas.

Survivors are loaded onto a bus by the apparent rescuers. They leave the underground complex. Thomas holds Chuck's body and cannot speak. In the novel's final revelation, the reader learns the rescuers work for WICKED — the escape was the last phase of the test.