Thomas (Dylan O'Brien) wakes up in an ascending elevator. With him are supply containers marked WCKD. When the elevator reaches the top, a door above him opens and he's surrounded by a Lord of the Flies type gaggle of young men/boys. Thomas takes off running, but stops when he realizes he's in a small glade surrounded by huge walls.
Gally (Will Poulter) subdues Thomas and keeps him from trying to run into a maze which is accessible through a door in the wall.
The leader of the group, Alby (Ami Ameen), and his consigliere Newt (Thomas Brodie-Sangster) explain the situation to Thomas. Once a month the elevator (or the box as they call it), comes to the surface with supplies as well as a new boy. They all live in the glade and call themselves Gladers. None of them can remember anything about their pasts or why they were sent there, but after a few days their names come back to them. Each boy is given a different job. Some are builders, some are runners. A door opens in the giant wall every day and closes every night. The door leads to a maze that surrounds the glade. Runners go through looking for a way out. "If you're trapped in the maze over night, the Grievers get you and you die". The maze changes every night. Alby was the first boy to arrive in the Glade. No one knows why they're there.
Thomas starts to form a friendship with the kid who came up the month before him. He's one of the youngest of the group. His name is Chuck (Blake Cooper).
That night there's a celebration for Thomas. Gally is wrestling one of the other boys and asks if Thomas wants to have a go. They end up sparring and when Thomas hits his head on the ground, he remembers his name.
That night Thomas has a dream. It's full of fleeting images, but a woman (Patricia Clarkson) says, "Wicked is good."
Alby takes Thomas around to show him more of the sites. The boys carve their names on the wall when they arrive. When one dies, they cross off the name. Thomas tries to fit in and he's given the task to go dig up fertilizer from out in the woods. While he's there, he's attacked by Ben (Chris Sheffield) one of the Runners who was stung by a Griever. While they fight, the other boy says, "This is all your fault. I saw you. That boy has what they call The Changing. A sting will apparently cause tremendous pain and make you prone to violence. There's no cure for it, so they force the boy into the maze at night just as the doors are closing." Everyone is concerned that there was a Griever attack during the day.
That night Thomas has another dream. It's more of the lady assuring him that Wicked is good, but now he also remembers himself and a girl about the same age sitting across from each other at work stations going over diagnostics.
The next day, Alby goes into the maze to retrace Ben's path and find out what happens. It rains during the day. Now it's getting late and Alby still hasn't returned. All the boys gather around the entrance to the maze. Just as the doors are about to close, the lead Runner named Minho (Ki Hong Lee) appears with a very injured Alby. Thomas rushes into the maze to help them, but the door closes behind him.
Minho and Thomas use vines to suspend Alby's body and try to keep it safe from the Grievers. Alby was stung while inside the maze. One of the Grievers appears and chases after Thomas. The Grievers looks like gigantic bedbugs with robot legs and scorpion tails. Thomas and the Griever run around a bit as the walls in the maze change. Finally Thomas is able to lure the Griever between two walls that are colliding and SQUISH! Dead Griever.
The next day Gally calls for a meeting of the Gladers. Most are excited that Thomas killed a Griever. There's another group though, lead by Gally who feel that the rules they have were put in place to keep everyone safe and ever since Thomas arrived things have changed like Grievers attacking during the day. And, speaking of things changing, the elevator arrives.
The boys run out to check what the elevator brought. Inside are no supplies, only a young girl (Kaya Scodelario). She looks up and says, "Thomas...", before passing out. In her hand is a note that reads: 'She's the last one ever.'
Gally calls for Thomas to be punished because non Runners are allowed in the maze. He doesn't like the fact that the girl knew who Thomas was. He's scared that the elevator hasn't gone back down since they took out the girl. Newt says Thomas can be locked up overnight without any food and starting tomorrow, he's a Runner. Gally is mad at his leniency.
A bunch of the boys go back into the maze, which further upsets Gally, to look at the carcass of the Griever. Inside it they find a weird device that has an electronic display reading the number 7. The device also is marked WCKD. The boys realize whoever sends them supplies also made the Grievers.
Minho shows Thomas a map of the maze. There are different outer sections that open each day as the maze changes. Each outer section is numbered. Last night, section 7 was open.
The girl is awake. She's at the top of a tower throwing stuff at the boys on the ground. Thomas yells up to her that it's him. She agrees to let him come up. He explains that her memory was wiped, but in a few days she'll remember her name. She says she already remembers her name. It's Teresa. She remembers Thomas too. He tells her that he's had dreams about her and a lady saying that "Wicked is good." When Teresa woke up she found two syringes in her pocket too.
That night, Thomas deals with his punishment of being locked up. Chuck visits him and brings him some food. He also asks Thomas to give his parents a little carved statue Chuck made. Even though he doesn't remember his parents, he's sure his parents remember him and miss him. Thomas gives back the statue and tells Chuck that he'll be able to give that to his parents himself.
The next morning Thomas and Minho go into the maze along with the device they got from the Griever. The device ends up making clicking noises and guides them to a new section Minho has never seen before. Minho is also concerned that all of the outer sections of the maze seem to be open. They get to a wide area marked WCKD Loading Dock that ends up in a dead end, but the device turns from red to green and opens a new path. That path leads to what looks like some sort of sewer tunnel. The edges of the tunnel have the same slime that the Grievers secrete, so they go back to the Glade.
Thomas decides to use one of the syringes on the still changing Alby. It ends up making him better. When he comes to he tells Thomas, "You were their favorite." But we don't find out what he means because outside doors all over the maze begin to open and out pour bunches and bunches of Grievers.
There's a giant Griever attack that wipes out a bunch of the boys and destroys much of their village. Alby is among the dead. Chuck is saved after getting grabbed by one of the Grievers. They end up hacking off its tail. After the attack, Thomas realizes that the venom from the Griever stings helps the victim remember. So he takes the hacked off tail and stings himself. He remembers a little bit more.
In Thomas' memory, the maze isn't a prison, it's a test. He sees all of the other boys in incubation tubes. A lot of them are in a panic. He also sees himself as a scientist along with Teresa.
The Gladers use the second syringe and Thomas is cured and confesses to everyone that he's one of the people responsible for everyone being there. Gally is furious and he and his group tie Thomas and Teresa to stakes outside the entrance to the maze as an offering. But, half the group is still with Thomas so they free them. Now the Gladers are divided.
Thomas tells Gally that he'd rather die trying to escape than die in the Glade not trying. Thomas takes a group into the maze. They get to the Loading Dock area from before and are attacked by a bunch of Grievers again. They go through the sewer tunnel type area and it leads to a locked door. Teresa needs a numerical code to get through. They realize the code must be the sequence in which the maze would normally open. She types it in and everyone goes through a door. Walls crush all the Grievers behind them.
The kids walk through some hallways until they find a door marked exit. (It's seriously a regular old exit door like you'd find in any office building). They go through and now they're inside the lab from Thomas dreams and memories. All the scientists are dead. A video starts to play.
The woman from earlier identifies herself as Ava Paige and tells the kids that they don't remember this but there was global devastation by something called the Flare. She was part of a controversial group called The World Catastrophe Killzone Department (WCKD), that believed that in testing the kids they could monitor their brains and find a cure. While she speaks, behind her guerilla soldiers rush in and start killing other scientists. She tells them she's glad they passed the first test and reminds them that Wicked is good. Before signing off, Paige shoots herself in the head.
A door opens leading outside. Before anyone can leave, Gally shows up. He has a gun. He says that they all belong in the Glade. He goes to shoot Thomas, but Chuck jumps in front of the bullet. Gally gets stabbed in the chest with a knife. Chuck hands the, now bloody, statue to Thomas and dies.
A group, who looks like the guerrillas from the video, rushes in and takes the kids outside to waiting helicopters. At first it looks like they're in the desert, but we pull out to reveal that they're outside what used to be a city. Buildings are destroyed and everything is covered in sand. They fly over the maze and the Glade and no one asks why the helicopters just didn't land inside the Glade and rescue the kids there instead.
In the final shot, it is shown that Paige is alive and wiping fake blood off her head. She says that the kids have taken the bait. More kids survived than she anticipated. The Maze was a success, and now "phase 2" can begin as the helicopter flies away to the city of ruins.
to open it.