Thomas wakes up in a swaying metal elevator, cranking upward in darkness. The only thing he remembers is his first name. When the elevator clanks to a stop, the doors at the top are opened, revealing a group of boys. They pull Thomas up with a rope and sat "Welcome to the Glade."

Thomas finds himself in a giant, square courtyard surrounded by 100 foot stone walls. Thomas also sees crops, animals, a forest, and a wood building. There is 60 jostling, joking boys who call him "shank", "shuck" and "green bean". Thomas meets Alby and Newt, Alby promises to show Thomas a tour the next day.

Thomas sees a metallic buy on a tree, and Chuck tells him its a beetle blade and will sting if touched. The shrieking comes from a wood house, and Chuck tells Thomas that the person screaming is a boy named Ben who was "stung" by a "Griever". Thomas enters the three story wood house searching for answers.

Chuck and Thomas eat ham sandwiches beneath a tree, Thomas then asks about the doors to the maze. Chuck explains that the doors close at night, which surprises Thomas. Thomas and Chuck watches four boys run into the maze. Chuck then tells Thomas they are called the Maze Runners.

Gally tells Thomas that he knows he is trouble because of what he saw during his Changing. Thomas is then struck by the feeling that hes been in the Glade before. He struggles to remember anything specific about his life before the Glade. He then tells Chuck he wants to be a Maze Runner.

Newt wakes Thomas up before dawn and leads him to one of the walls, where Thomas sees small, pulsing red lights. Newt then shows Thomas a creature that is a "horrifying mix of animal and machine". The creature, which has long metal arms that end in saws and other terrible implements. Newt explains to Thomas that its a "Griever" and that they come at night and patrol the Maze.

Alby gives Thomas a tour of the Glade, showing him the gardens, the homestead, and the Deadheads forest. Thomas experience moments of recognition and familiarity. Alby tells Thomas that the walls inside the Maze shift every night, which is why the Gladers haven't been able to identify a way out. Alby says the beetle blades are how the Creators watch the boys. The tour is then interrupted by a loud alarm.

When the Box reaches the surface, there appears to be a dead girl inside. Alby and Newt bring her up and confront Thomas, asking if he knows her, but he denies it. The girls arrival is a strange and unexpected break in pattern, before every month one boy comes every month, and supplies every week. The girl wakes up and then mumble "Everything is going to change". Then she falls and a paper is in her hand that reads "She's the last one ever."

Alby has the girl checked out by the Med-jacks, boys who act as doctors, who determine she is in a coma. Thomas thinks that the girl is familiar and knows his fate is somehow tied to the girls arrival. Alby then calls a gathering, which is a meeting of the Keepers, the leaders of each profession or group.

Thomas goes deep into the woods and discovers the graveyard with makeshift marks. Just then, a Glader breaks through the woods and attacks Thomas, biting him on the shoulder. The two struggle, and when Thomas throws off his attacker, he realizes it is Ben.

Ben’s ropy veins show through his pale skin, and his eyes are bloodshot. He’s carrying a knife. Alby appears, threatening Ben with a bow and arrow. Ben tells Alby that he should kill Thomas, saying “I saw him,” and “he’s bad. We have to kill him!”. That night, Thomas can’t sleep, and in the morning, he has a bad headache and heartburn. Nonetheless, Thomas goes with Newt to the Blood House and spends the morning working with the acne-covered Keeper, Winston, taking care of the animals and then butchering a hog.