The Maze Runner starts with a young man (surprise!) regaining consciousness in a cagelike elevator. He doesn’t remember anything, not even his own name. When the elevator reaches the top, our protagonist encounters a tribe of other boys of varying ages, all of whom live in a verdant, square enclosure known only as the Glade. The boys call him Greenie or Greenbean, which is a reference to his recent arrival. He doesn’t like the name too much, but it’s all he has.
Soon he learns that once a month, the elevator, which the Gladers call the Box, brings two things to the Glade: food and supplies, and another Greenie. And all Greenies soon learn the three rules of the Glade–1) Do your part; 2) Don’t hurt a fellow Glader; 3) Don’t go outside the Glade unless you’re a Runner. Naturally, our protagonist is curious what is on the outside, but Alby, their leader, tells him not to worry about it. Later on, Chuck, who was the previous Greenbean, lets it slip that the Glade is surrounded by a colossal Maze. The Maze has one door, which closes every night. If you’re stuck outside the Glade when the doors close, you have to contend with the Grievers, hideous, sluglike creatures that eat Gladers for breakfast. And that, boys and girls, is why you don’t leave the Glade unless you’re a Runner.
That night, the Gladers throw a huge party in our protagonst’s honor, during which Newt, who acts as vice mayor, explains life in the glade. He reveals that the Maze changes every night, but the Runners explore it every day, mapping and memorizing it, trying to find their way out. They’ve been at it collectively for three years. As newt explains the occupational system, our protagonist reveals that he wants to be a Runner, and Newt calls him crazy, but says that people don’t choose to be Runners; rather, they are chosen by the leadership.
During the celebration, our protagonist remembers his name–Thomas–while wrestling with Gally, a boy whose eyebrows must have been surgically sculpted into a frown. With this, officially becomes a part of the group. But things begin to change, and it doesn’t take long at all. First, one of the Runners, Ben, gets “stung” by a Griever in broad daylight, and he attacks Thomas in the forest, saying, “You did this! It’s all your fault!” Out of necessity, the Gladers banish him to the Maze, and the next morning, Alby takes his place. The same thing happens to Alby, and Minho–the Keeper of the Runners–knocks him out and carries him back to the Glade, but by the time he is within sight, the doors are already closing, and neither one will make it. So Thomas decides to do something drastic, and he bolts through and makes it into the maze with Minho and Alby just as the doors close.
This is where we first see the Grievers. More on this later. After securing Alby for the night, Thomas finds himself in the sights of a Griever, and it chases him through the Maze. As he escapes, Thomas lures it into a rapidly closing section of the maze, barely making it out alive. The same can’t be said for the Griever, who didn’t stand a chance against the wall. The next morning, Thomas and Minho bring Alby back to the Glade, and the elevator arrives once again. But it isn’t carrying supplies; the only thing inside is a young woman, Teresa, who is carrying a piece of paper that says, “She’s the last one. EVER.” She wakes up, and recognizes Thomas by name.
Thomas, Minho and some other Gladers decide to go investigate the dead Griever. They manage to pull some sort of device from its remains, which turns out to be an access key used by the Grievers to enter and exit the Maze. When they get back, Teresa is at the top of the lookout tower chucking rocks down at the boys, wanting to be left alone. But she does allow Thomas to come up, and she gives him a pair of syringes that turn out to be the antidote for the serum that the Grievers inject into their victims. They give one to Alby, and Newt makes Thomas an official Runner.
The next day, he and Minho go and check out the section of the Maze that the dead Griever had come from. They find the Griever hole, and when they approach, an IFF device scans them, and since they obviously aren’t giant slugs with mechanical spider legs, it sounds the alarm, sealing that section of the maze. In the meantime, Alby wakes up with his memory partially restored. He says the same thing Ben did earlier, that Thomas was involved in whoever was sending people up.
That night, all four of the Maze’s egresses open, and Grievers flood into the Glade. Newt, Chuck, Teresa, Thomas, and some others huddle inside the town hall, and one of the Grievers breaks through the roof and grabs Chuck with the claw at the end of its scorpionlike tail. Alby intervenes, whacking the tail with a machete until the Griever releases chuck. Another Griever then grabs Alby and carries him off.
In the scuffle, the syringe full of Griever serum got knocked off the stinger, and Teresa grabbed it before they all went out to survey the carnage. Gally, who has been blaming Thomas for everything that goes wrong, walks up and decks him, laying the blame on him again. Thomas concludes that he must be right, and he takes the serum from Teresa, injecting himself so that he can regain some of his memories. And this serves to confirm what his dreams have been telling him: the whole time everybody was in the maze, he and Teresa were working behind the scenes with WICKED, whoever they are.
When he comes to, Newt tells him that Gally has seized control, and they’ve gone along with him, lest they be banished with Thomas that night. But after a bit of convincing, they side with Thomas again and go with him back to the Griever hole, all the while running from the creatures. Instead of scanning them, this time, a screen flashes to life asking for an eight-digit code, which Thomas guesses is the order that the various outer sections of the Maze open. Minho, who knows the Maze better than anybody, gives Teresa and Chuck the code, and they put it in. The screen turns green, and what’s left of the group falls through a trapdoor into some sort of facility.
They walk around and find tons of dead bodies and a video recording wherein Ava Paige, the chancellor of WICKED, explains everything: war, apocalypse, zombies, ethically dubious tests and experiments on those who were immune to the zombie virus…you know, the usual. Throughout the video, the personnel can be seen working frantically in the background, and at the end of the video, soldiers infiltrate the facility, guns blazing, killing all in sight. At the end of the video, Paige commits suicide, her last words being, “WICKED is good,” the mantra the subjects were taught over the course of the tests. Immediately after the end of the video, a set of doors to the exterior opens, and the group prepares to head out. But Gally, who stayed behind, decided to brave the Maze, got stung by a Griever, and made it all the way to the facility. He’s got a gun, and he’s determined to make Thomas pay for what he’s done. He raises the pistol and fires just as Minho puts a spear through his heart. Thomas escapes unscathed, but only because Chuck jumped in front of the bullet. As he succumbs, the exterior door opens and several soldiers come in to take the boys and Teresa to safety.
As they pile into the chopper, we see Ava Paige wiping the fake blood from her temple and addressing a committee of some kind. The Maze trial is over, she explains, and the subjects are showing promise, most notably Thomas. Now begins Phase 2. Roll credits.