The Maze Runner is a young adult dystopian novel set in a post-apocalyptic world. The story begins in a dark metal elevator, where a teenage boy awakens with no real memories other than the fact that his name is Thomas. When the elevator stops and the doors open, Thomas finds himself surrounded by teenage boys. Their leader, a boy named Alby, welcomes Thomas to the Glade. Thomas quickly sees that the Glade is surrounded by high stone walls covered in ivy. The Glade, in fact, appears to be a large square piece of land with a few scattered buildings. In each of the four walls, there is a narrow opening.

Over the course of the next few days, Thomas learns that behind the walls lies the Maze, which as its name implies, is a massive labyrinth. The Maze is filled with Grievers, horribly violent mechanical creatures that only come out at night. Since the openings into the Maze, the Doors, close at night, the Grievers cannot get into the Glade. During the day, a group of Gladers known as the Runners navigate the Maze in the hope of finding an exit. On the same day every month, the elevator, called the Box, brings a new teenager, and supplies are delivered every week. On the day after Thomas arrives, however, the Box uncharacteristically returns with another teenager—the first and only girl to arrive in the Glade—who appears to be in a coma.

The next day Alby, the leader, and Minho, the Keeper of the Runners, go into the Maze to investigate a dead Griever that Minho found the previous day. Just before the Doors close for the night, Thomas sees an exhausted Minho dragging an unconscious Alby towards the Door. With no one around to help, and with the fear of breaking the number one rule, which forbids Gladers to enter the Maze at night, Thomas slips through the Doors to help Alby and Minho just as the Doors close. Minho tells Thomas that Alby was stung by the “dead” Griever, and that now all three of them have no chance of surviving the night. Thomas and Minho eventually lure a group of Grievers away from Alby’s body and towards the Cliff, a mysterious place in the Maze where the path ends in an empty expanse of gray light. As the Grievers charge the two boys, they dive out of the way and cause the Grievers to disappear over the Cliff.

By the time Thomas and Minho arrive at Alby’s body the next morning, the Doors are open again and the other Gladers are staring at the boys in disbelief—they are the first people to ever have survived a night in the Maze. Newt, Alby’s second-in-command, has Alby taken to receive the Grief Serum, which causes the ailing leader to undergo the Changing. The Changing is a painful side effect of the serum that causes the Gladers to recall some of their life before the Maze, and no one ever is the same afterwards.

The next few days bring a string of first events for the Gladers. The girl, whose name is Teresa, wakes up from her coma and it is revealed that she has been sent as a trigger for the ending. She tells Thomas that the Maze is a code. Also, the sun disappears, which causes the crops and animals to dwindle and, most significantly, causes the Doors to remain open at night. The Grievers enter the Glade on the first night after the sun disappears and carry of a boy named Gally, who tells the Gladers before he is taken that the Grievers will only take one boy per night until the end.

The next day, Thomas uses the Maps that the Runners create every day to figure out that the Maze’s walls have been repeating words: FLOAT, CATCH, BLEED, DEATH, STIFF, and PUSH. To better understand what the code means, Thomas purposely gets stung by the Grievers to go through the Changing in an attempt to regain his memories. After he recovers, Thomas tells the Gladers that in order to escape they must punch the code into a computer station by jumping off the Cliff and into the Griever Hole, an invisible portal. 

After finally convincing the Gladers to follow his plan, Thomas helps to lead an armed band of Gladers into the Maze. At the Cliff, the Gladers find a group of Grievers waiting for them, while other Grievers cut off their escape. The Gladers find that they must fight for their lives and make a way for Thomas and Teresa to get inside the Griever Hole. When they finally make it inside, they use the code and effectively shut down all the Grievers and the Maze.

The surviving Gladers join up with Thomas and Teresa inside the Griever Hole, and a long, slimy slide brings them all into an underground compound where they come face to face with the Creators, who sent them into the Maze. A woman with the word WICKED stitched on her shirt approaches them with a hooded teenager, and congratulates them for having survived this far, but says there is still one more test. The teenager reveals himself to be Gally, and throws a knife at Thomas while under some sort of mind control. Chuck, a fellow Glader, jumps in front of the knife to save Thomas. As Thomas mourns Chuck, a new group of men and women enter the compound and shoot the woman, as well as the rest of the Creators. The rescuers shuttle the Gladers onto a bus, where they drive through a post-apocalyptic landscape.

The Gladers are told that there has been an ecological disaster, known as the Flare, which has caused widespread death and a disease. WICKED’s intention is to raise children in the harsh environment of the Maze to test their resilience for hope. The group that rescued the Gladers is opposed to WICKED’s inhumane treatment of children and they bring the Gladers to a safe-house, where they are given food and beds.

The novel ends with a memo from the Chancellor of the Maze Trials, Ava Paige, writing that the boy’s murder and “rescue” was a good finale to the experiment. Ava then writes that after the group gets a good night’s rest, they will proceed with stage 2 of the experiment.