| Spoiler Alert!|
This page contains details about the plot which may lower your enjoyment of the books and/or movies. Discretion is advised.
Thomas wakes up in a metal lift, only remembering his name. A group of boys pull him out and tell him he is in the Glade, the part of the maze they live in. Thomas discovers that the Gladers have been trying to solve the Maze for two years. He also finds out that the Maze is inhabited by monsters called Grievers, which are half-animal, half-machine creatures that are extremely dangerous. However, they only come at night. He finds out that at night time, the walls of the Maze, called the Doors, close to protect the Gladers from the Grievers outside. Thomas is the main protagonist of the series.
He makes a friend named Chuck, and an enemy, Gally. While Thomas has no memory of Gally, Gally has endured the Changing and claims that he knew Thomas and that Thomas is evil. The Changing is a process that occurs when someone is stung by a Griever, one of the sinister creatures that inhabits the maze. The Changing causes almost unbearable pain, but also gives the Gladers back a piece of their memories.
As a Greenie, Thomas has much to learn. In the first day, only a newer Glader named Chuck reaches out. Survival in the Glade requires following some harsh rules learned from necessity. Each day "Greenbean" Thomas will have to train with a different Keeper, (Keepers lead the different work divisions and are the highest members of the Glade). Despite his lack of memory (and contrary to advice), Thomas feels a strange urge to become a Runner - one of the boys who explores the Maze.
The next day, a girl arrives in the Glade via the lift, which is unusual first for being off schedule and then because the Glade comprises only boys. She says that " Everything is going to change" before going into a coma. There is also a note in her hand, which says that :" She is the last one. Ever."
Thomas then sees Minho, the Head of the Runners, and Alby, the Leader of the Gladers, struggling to make it back out of the Maze before the Doors close for the night. Alby has been stung by a Griever and is barely conscious. Thomas breaks the Glade's number one rule and steps out into the Maze, hoping to help Minho and Alby. However, all three get stuck outside the Glade, and thought they are going to die, because no one has survived a night in the Maze before.
Minho panics and runs off. However, Thomas ties Alby up on the wall to protect him from the Grievers. He then diverts the Grievers away from Alby. Minho reappears and both of them trick the Grievers into jumping off the Cliff, thereby surviving the night in the Maze.
In awe of their survival, the Council of Keepers nonetheless agrees it must judge Thomas for all the trouble and rule breaking he has brought them, and consider his punishment. Gally must leave the Council meeting after actively threatening to kill Thomas. The remaining Council decides Thomas can stay and that, after one day in the slammer, the Glader's jail, he should become a Runner and Minho will train him.
Minho teaches Thomas what the Runners do in the Maze, especially map-making. He tells Thomas that all the Runners make maps for the section they are assigned to. They then study the Maps and try to figure something out. Thomas also discovers that he can talk to the girl telepathically, and finds out that her name is Teresa. She wakes up one day, and says that she triggered the Ending.
The very same day, the skies turn gray and the Doors stop closing, thereby condemning the Gladers to the mercy of the Grievers. Gally shows up that night when the Grievers attack and says that the Grievers will only kill one person a night, then jumps on a Griever and is carried away. Thomas, Teresa, Minho and Newt then figure out that the Maze spells a code, and find out what the code is using the Maps of the different sections.
Thomas gets stung by a Griever on purpose, and goes through the Changing. He gets back some of his memories, and tells the Gladers what he learned. He tells them that the only way out of the Maze is through the Griever Hole, over the Cliff where the Grievers live. Then, most of the Gladers decide to follow through with the plan, and they prepare to go into the Maze that day. They then fight the Grievers at the Cliff, so that Thomas, Teresa, and Chuck can get into the Griever Hole and punch in the code. Half of the Gladers die fighting the Grievers, but after Teresa enters the Code that stops the Grievers, the remaining 20 manage to escape through the Griever Hole and open the door out of the Maze.
The surviving Gladers find themselves in a chamber and meet the Creators, the people who sent them to the Maze. A woman comes out and tells them that they passed the Maze Trials, however that there is one Variable left. Suddenly Gally appears and throws a knife at Thomas. Chuck dives in front of Thomas, sacrificing himself to save Thomas. Thomas breaks down and cries, because he had promised Chuck that he would take him home, and then knocks out Gally. A group of people, the Rescuers, burst into the chamber, kill the Creators, and tell the Gladers to run with them into the real world. As they all rush onto a bus with the Rescuers, a sore-riddled woman attacks Thomas; the driver runs over the woman with the bus.
One of the Rescuers then explains to Thomas and Teresa why they were put into the Maze. She says that when Sun Flares slammed into the Earth, countless miles became wastelands and millions of people died instantly. Then came a sickness called the Flare. She explains that the physical effects of the Flare, such as sores, are caused by something else, but the Flare lives in their brains, and causes them to slowly go crazy, finally consuming them and causing them to lose their humanity. Everything the Gladers went through was a test, planned out and their reactions recorded, all in an attempt at finding youth capable of helping to beat the Flare.
The Gladers are then housed in a building where they think they are finally safe. The next book starts the next day.
Book retailer Barnes & Noble included the book as part of its showcasing of new writers for the end of 2009 and the beginning of 2010. Kirkus Reviews wrote, "Hard to put down, this is clearly just a first installment, and it will leave readers dying to find out what comes next".
Jessica Harrison of the Deseret Morning News labeled The Maze Runner as "a thrilling adventurous book for kids ages 13+ that will get readers' hearts pumping and leave them asking for more." She noted that it "starts out a bit slow" but as it matched Thomas's confusion and picked up pace as he became more accustomed, she wrote that "it's almost as if Dashner is easing the reader into what becomes a fast-paced, nonstop action." However, she thought the "only drawback" was the "fictionalized slang" that although it "feels realistic and fits with his characters, it gets old pretty fast. On the plus side, however, it's used so often that the reader almost becomes desensitized and learns to ignore it."