The story starts off with a boy named Thomas who wakes up in a metal box, he doesn't remember anything about his past or anything at all, except his name. When he steps out of the metal box he finds himself in a strange place called the glade. There are about 50 other boys who've come to the glade who also don't know about there past, who called themselves the gladers. He then meets the leader of the gladers, a boy named Alby and another boy named Newt. Then there's Chuck, the last "newbie" to come to the glade who becomes good friends with Thomas, at the time, the only friend he had.

As time goes by, Newt explains why the glade was there and what its purpose was. The Glade is in the shape of a perfect square forming a box around the gladers, and outside the glade is the maze. There are keepers who are in charge of certain things around the glade. The most important people in the glade are the runners, the ones who go out running through the maze. The Gladers' number one goal, is to solve the maze, and find their way home.

Their is one threat stopping them from figuring out the maze, one threat stopping them from going out at night and from going too far into the maze, horrific animals that go by the names of grievers. Giant bug-like creatures that are strongest at night. Thomas, on his first day, finds out that if get stung by a griever you go through a process called the changing. As Thomas's experience continues, he starts feel as if the glade is somewhat familiar, as if he's been there before, and out of the blue has a sudden urge to become a runner. Then things start to change..

One day after Thomas's arrival a new person shows in the metal box. The gladers expect a new boy to come to the glade every month on the same day, so it was definitely a surprise to them. Not only did the person come earlier than usual, but the new glader was a girl. At first the girl looked dead, but was discovered that she was in a coma. When she woke up, she only opened her eyes for 3 seconds and mysteriously said, "everything is about to change". She also came holding a message on a piece of paper, it said, "she's the last one, ever". The girl is put into a medical room until further notice. .

The next morning the new girl woke up at last, and has a special gift, she can talk to Thomas in his mind. Then things start to fall apart, the screen turns grey as if it were a screen, and on that night, the gates did not close. The grievers had complete access to the glade, and attacked it. During the attack a boy named Gally came to a place where a few gladers were hiding and said that the grievers would kill one glader every night. After three days, three gladers died, and that's when Thomas came up with a terrible idea. He would have to Get stung by a griever on purpose and go through the changing,get his memories. Thomas's idea was a success and finds out very bad things about him and Teresa.