Thomas arrives in a boxed shaft in a maze. The leader of the group is Alby and there are runners where an Asian boy named Minho is the leader. The second in command after Alby in the maze is Newt. The whole people in the maze strictly follow their leader and follow the rules and regulations without questioning.
The initiation night there is a bonfire and a boy named Gally is fighting with a boy and the boys are surrounding the fight. It’s a friendly fight. Everyone calls Thomas by different names such as shank, greenie, slint etc. Thomas is called by Gally to have a friendly fight. Gally hits Thomas and he lands his head on the floor making him remember his name “Thomas”.
As no one knows what Thomas is good at he works at the garden with Newt. He is asked to bring fertilizers from the jungle. He goes and is attacked by Ben. His skin is different and his vein is greenish. Ben questions Thomas “why did he do this to them?” Ben attacked so he is banned from the glade.
Next day Alby and Minho visit the maze and come back. All of the gladers see that Alby is stung by grievers. The glade doors are closing and as all strictly follow the rules no one goes for help except Thomas. The door closes leaving Alby, Minho and Thomas stuck in the maze for the night. Till now no one has survived a night in the maze.
Thomas hangs Alby up with the vines. Then killing a griever Thomas, Minho and Alby survive the night and return to the maze. When they return Gally doesn’t believe Thomas as good and innocent. He mentions how with arrival of Thomas things have started to change. Then the shaft opens and for the first time they see a girl with a note in her hand saying “She is the last one”.
Then Minho shows Thomas the maze miniature version and explains that door has a pattern. The girl wakes up and Thomas starts hearing noises. He hears WICKED is good.
Alby wakes up form the stung from griever and explains that he saw Thomas when he was stung. He mentions that Thomas was always their favorite. He gets cured with the serum that the girl brought with her. Thomas is punished as he broke the law and went inside the maze. But, with Minho’s request he is considered as one of the runners. His friend a Chuck mentions and shows a small pendant that is his parent’s remembrance.
The next day the door opens and the maze starts changing by itself. The maze door does not close and it is already been sunset. Then they hear grievers and they all go to hiding. Then most of the people die. Saving chuck Alby gets taken by the grievers. As Alby is hanging in the hands of grievers he says that Thomas has to save all of them.
Thomas gets hit by Gally. Then Thomas finds a serum and hits himself with it so that he can remember something. Then he sees how Teresa (the girl) and he are part of WICKED and all of this is done by them too. He also sees a women saying to him WICKED is good. He confesses everything to Newt and the remaining boys.
Then there are two groups formed the next day. One headed by Gally and then after confession the other group is held captive. But, they take control and decide to leave the glade. Gally and his men decide to stay in the glade.
Out in the maze they are attacked and many of them are killed in the process. Then they reach and find the end. Then there is a code to be entered and it is revealed that the maze itself is a code. The maze pattern opens when they push a red button.
They enter and a women projects and says how things have changed. There is no earth the drought and virus has killed everything and flare has started. The people who survived are the new generation. Saying this she kills herself.
Then Gally comes stung by a griever. Then he tries to attack Thomas and he says he has to do it. It looks like he is being controlled. Then Chuck dives and saves Thomas and gets himself killed. In the meanwhile Gally is hit by a big javelin.
Then people come and take all of them saying they have to trust them. They are there to save them all. When they reach outside all is desert. The man says “Everything is about to change.” All of them are put in a helicopter and they leave. Thomas and Teresa talk telepathically.
The woman who killed herself is shown wiping her head stating that the video which gladers saw was fake. She is addressing many people who are sitting in a conference room. She says that many children survived than what she had expected. She ends by saying now we have to start “TRIAL 2.”