Awakening in an elevator, remembering nothing of his past, Thomas emerges into a world of about thirty teenage boys, all without past memories, who have learned to survive under their own set of rules in a completely enclosed environment, subsisting on their own agriculture and supplies. With a new boy arriving every thirty days, the group has been in "The Glade" for three years, trying to find a way to escape through the Maze that surrounds their living space (patrolled by cyborg monsters named 'Grievers'). They have begun to give up hope when a comatose girl arrives with a strange note, and their world begins to change with the boys dividing into two factions: those willing to risk their lives to escape and those wanting to hang onto what they've got and survive.

In the epic finale to The Maze Runner Saga, Thomas leads his group of escaped Gladers on their final and most dangerous mission yet. To save their friends, they must break into the legendary last city, a WCKD controlled labyrinth that may turn out to be the deadliest maze of all. Anyone who makes it out alive will get the answers to the questions the Gladers have been asking since they first arrived in the maze. Will Thomas and the crew make it out alive? Or will Ava Paige get her way?