Thomas wakes up with no memory except his first name,Thomas, of his previous life in a elevator. He finds himself living in the glade and trying to escape the maze. Then, a girl comes up from the box holding a note saying that she was the last one ever, and they find out how to get out of the maze. When they get to the Griever Hole, they have to kill grievers and then they deactivate the maze. They get to the creators, and find out there is a disease called the "flare" in the real world that kills people and turns them into zombie looking people before they die. then the story ends at the boys resting in a house not infected by the "flare".