Thomas wakes up to find himself in a box. When he reaches the top, he is pulled out by a group of boys. The only thing he remembers is his name, nothing else.
Thomas learns that all these boys live in a place called the Glade. The Glade is surrounded by tall, stone walls with four massive openings (also referred to as doors) in the center of each wall. These doors close each night to protect them from the monsters that live beyond the Glade's walls. The monsters live in a place called the Maze which lies outside of the walls around the Glade. These monsters are called Grievers and attempt to sting the Gladers. If the Gladers get stung, they undergo the Changing, a painful process which people can survive if given a special serum in time. This serum has some side effects such as regained memory. The walls to the maze move every night so there is a different maze outside each door every day.
A day after Thomas arrives at the Glade, another person is sent up in the Box, the elevator which brings new people to the Glade. Only boys live in the Glade and to their surprise a girl, Teresa, is sent up in the Box. They were also surprised because it was the first time someone new had been brought to the Glade in less than a month. She brings with her a message that she will be the last one to ever arrive in the Glade and that the end is nearly coming someday soon. She then falls into a deep coma. After the arrival of Teresa, the boys blame Thomas for everything abnormal going on, saying everything is all his fault.
In the end, the boys realize that they are against a force called WICKED. The boys believe that they are being put through a series of trials to find the best boys for the job WICKED has planned for them. They realize that the Maze is to be solved.
People called Runners, have studied the maze for the two years, running around their section of the maze each day. Every day the Runners go into the maze and look for changes in the maze. They come back to the Glade and sketch the days changes. Teresa has a telepathic connection with Thomas and tells him that WICKED is good, and that the maze is a code, and meant to be solved. Thomas is completely scared to tell the others about their Gift, and other people, who have gone through the Changing, claim to have seen Thomas before. In an effort to bring memories back about who Thomas really is and why the Gladers are there, Thomas purposefully gets stung by one of the Grievers. During the Changing Thomas understands why they are there. He and the girl Teresa both helped design the maze, and Thomas finally understands how to escape the Maze. He gets all of the sketches of the maps of the Maze and stacks them over each other for each day and for each section of the Maze that day on wax paper. The maps start to spell a series of words which have to be entered into a computer through an invisible hole off the Cliff, which lies somewhere in the maze. Everyone realizes this plan and Thomas takes a group and leads their final charge against WICKED and in the end types the words in and pushes a button and a door opens letting the remaining 21 Gladers through.
They all meet the Creators of the Maze. Gally, a crazy Glader who had mysteriously disappeared at one point, throws a knife at Thomas, but Thomas's friend, Chuck, intercepts it, sacrificing himself. The remaining Gladers are soon taken by a bunch of people that come in and kill the Creators. They find out that the Earth is now a barren wasteland, burned by sun flares. A disease spread, the Flare, and consumed almost everybody on Earth. WICKED set up the maze to find the smartest people to find a cure to this disease. A group of people who are completely against the idea of WICKED get Thomas and the others away from the Creators. Thomas and his group are told that they are heading across an extremely dangerous part near the equator, called the Scorch, to get to a safe haven to find the cure. Thomas and his friends are given shelter, beds, and food, and fall into a peaceful sleep. Little did they know what would be awaiting them when they woke up.
In the epilogue, the head leader of WICKED, in a couple of memos, describes how group A's trial results went extremely well in the Maze, and that their next challenge will be to cross the Scorch. Thomas and his friends will be given one day of rest before the second stage of the trials begins.