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 be where the Grievers leave the Maze or "The Griever Hole" as he and Minho call it. If they can come and go over the edge of the Cliff, then maybe so can the Gladers. This drives Thomas to think they need memories to get out, so he intentionally gets stung by a Griever so he can go through the Changing – the process that people go through after getting the Grief Serum, a syringe of medicine that arrives in the Box along with the other supplies and is administered to people who have been stung by Grievers. The Changing can trigger memories and most often does.

Thomas and the Gladers find out what the pattern is, which causes most of the Gladers to decide to make a run for the exit, knowing that it could be suicidal trying to take on the Grievers, but figuring that nothing could be worse than being stuck in the Glade waiting to be hunted by the Grievers. They succeed, only to find out that they were test subjects in an experiment conducted by an organization 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 laboratory 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 throw a knife at Thomas, but Chuck, the youngest Glader and Thomas' friend, jumps in front of him.

After briefly mourning the death of Chuck, all 20 Gladers are rescued by a group of people and brought to a safe haven while being told about catastrophic solar flares that caused an apocalyptic event, followed by a disease called the Flare, that killed millions. The rescuers reveal that orphaned children are being tested to find a cure for the virus.