A boy named Thomas wakes up in a metal box. He doesn’t remember anything except his own name: his mind is totally cleared of any memories that could give him clues about his past life and about himself. The box suddenly opens and Tom understands that he was in the unlit elevator. Behind the elevator doors there are other teenagers who also do not know anything about themselves. They introduce Tom to the place called the Glade - a huge square-shaped space surrounded by the enormous stone walls hundreds of meters high that move every night. The Glade is a small farmer community of roughly fifty kids calling themselves Gladers.
The community is ruled by two older boys: Alby - the leader and Newt - his second-in-command. Both boys are enforcing strict rules keeping the other Gladers busy all the time gathering food and repairing structures. But despite Alby’s short temper, he is the most experienced glader and he really knows that idleness will erode the small society he managed to built, so he does it for good. Newt, though looking as Alby’s dumb muscle at a first glance, is a reserved and competent person who is ready to step in every time when Alby needs help or he needs a voice of reason and common sense contrary to his impulsive decisions. Their relationship are operating on mutual respect and the Glade survives under their rule for a long time.
Thomas also meets other Gladers - lots of them, we’ll tell you more about them when the plot unfolds - who he will live with from now on. Alby assigns a guide to him, so that the newcomer can accommodate faster. The guide’s name is Chuck, he is one of the youngest Gladers. Chuck is chubby, clumsy, naive, very talkative up to being annoying, but he does know a lot of valuable informations to give.
From him Thomas learns how the Glade operates: every month a newcomer arrives via the elevator and every weeks the supplies are found in the same elevator. No one knows why it works that way, so the boys just try to survive and find the exit from the Labyrinth that lies behind the Glade. It is seemingly endless space, the maze of the everchanging stone walls covered by vines. The Labyrinth is inhabited by dreadful and deadly monsters - Grievers, a cross between machines and living creatures who kill any fool deciding to spend the night in the Labyrinth. Every night the walls move closing all the entrances to the Glade and protecting its inhabitants from the outside dangers.
The Gladers who map the labyrinth are named Runners - they do exactly what they are named for, they run as fast as they can trying to avoid the Grievers, try to figure the patterns of the maze walls and find the way to the outer world. The Runner’s duty is the most dangerous of all, because even the ones who are just slightly injured by the Grievers, will undergo the painful process of Changing that will temporarily return them some of their memory.
There are plenty of professions Thomas can apply to - cookers, gardeners, farmers and so on. But the boy is mostly interested in becoming a Runner. However, their leader Minho is not an easy person to get along with, so at the initial meeting he openly express his objections, not willing to see Thomas in his squad. Minho isn’t the only one suspicious. Some of the Gladers claim that they saw him Changing - that may mean that he is Grievers’ spy. The most unwelcoming is a dark-haired boy named Gally. He claims that he saw Thomas even before the Gladers took him from the elevator - in the Labyrinth, so he must be a Griever in disguise. But still he has no proofs and even Minho calls him out for such a ridiculous accusations.
Another boy who confronts Thomas is named Ben. Thomas sees him when he undergoes the Changing, screaming in pain. Suddenly, Ben attacks Thomas, claiming that now he remembers him and it’s all his fault. Attempted murder is a serious crime in the Glade and even Changing can’t be an excuse. Ben is exiled from the Glade to the Labyrinth - it means almost certain death.
Everything changes the next day after Thomas’ arrival. The elevator (called The Box by the Gladers) opens out of schedule and delivers another newcomer to Glide. But it is a girl - the first girl they see here. The Gladers don’t know how they shall react - to add more anxiety to them, the girl seems to be ill. She mumbles some words about she being the last one sent and the things coming to an end and collapses to the floor. She is in coma. The Gladers put her to quarantine under the care of the local medics (or Med-Jacks), Clint and Jeff and return to their daily activities. But Thomas can’t stop thinking about the girl. He is sure her name is Theresa and he knew her before he got to the Glade.
Girl or not, the life in the Glade marches on. Runners continue investigating the Labyrinth. One day Minho returns earlier than usual and reports to Alby that they have found a dead Griever nearby. Alby personally comes with Minho to investigate, but what seemed a corpse appeared to be alive and stings Alby. Seeing his leader in distress, Minho tries to rescue him, taking unconscious Alby to his shoulder and running back to the Glide. But it is too late and with the sunset the walls start to close the entrance to the Glade. Thomas sees this and, despite the strictest prohibition to enter the Labyrinth under any circumstances, runs to the rescue. The wall closes behind Thomas. Three young men are now trapped in the Labyrinth until morning… or until they are killed.
Surely, the Grievers soon track their prey and gather to attack. Minho runs away in panic, thinking that all is lost and they will have a slightest chance to survive if they split up. It’s Thomas’ turn to save Albi. He climbs the vines and distracts the Grievers who chase him now. On his way he sees Minho and shares his plan with the Runner. Together they lure the Grievers to the Cliff - a high place where a gigantic abyss is seen between the walls. Minho and Thomas jump aside at the last moment and Grievers who were chasing them, fall from the Cliff.
In the morning, when the wall opens again, the Gladers are amazed to see the heroic survivors. Still Thomas is imprisoned for breaking the rules, but now it is Minho who manages to take him out of prison using his authority. Minho also proclaims that Thomas now is officially a member of his squad in the rank of Runner trainee. The Gladers, mostly, don’t object - they feel that Thomas deserves such a promotion. Only Gally seems very unhappy: he is sure that they survived courtesy of Thomas being a traitor and now they all are doomed. Minho calls him out for such a ridiculous accusation and after a loud argument that almost turned to a fight, Gally runs to the Labyrinth and disappears there. No one stops him.
Alby is slowly recovering from his Changing. He also says that he saw Thomas before and Thomas is somehow responsible for the building of the Labyrinth (so was Ben exiled for nothing then?). Despite physically he is fine, the leader seems mentally broken in some way. He isn’t as confident as he was anymore. Thomas also visits Theresa who is still in the hospital and suddenly discovers that he has a telepathic bond with her, but he still doesn’t understand how it works. Frightened, he runs to the Labyrinth to escape her voice telling him the same thing he heard from Alby - Thomas and Theresa are somehow connected to Labyrinth creation. He returns soon and is jailed again for violating the rules - this time for real.
After the day of Thomas’ incarceration he begins his training as a Runner. Minho shows him the patterns of Labyrinth they already know and shares the tactic and secrets Runner have already learned. Thomas doesn’t see anything new, but the patterns trigger some thoughts in his head - they don’t look random and they may actually mean something.
Theresa comes to her senses and her first words are about she is the cause of the end of everything. And she is right. The sun stops its movement and the sky is replaced by an artificial grey background. What is worse, the walls don’t shelter the Glade at night anymore, which means the Grievers can now easily enter the Glade. At night they attack. Gladers are preparing to the hopeless last fight, but suddenly Gally returns. Half-mad he screams that the end of time has come and now the Grievers will take one victim every night until no one is left. He is the first one taken and dragged to the Labyrinth - and it seems he is right, the attack ends at once.
The next morning Thomas, assisted by Theresa, finally comes up with an idea. The Labyrinth is indeed a code. He finds the hidden maps collected by the Runners for all the two years that the Glade exists (Theresa for some reason knows their location), compares them and finds repeating patterns - they are words and letters. But they still can’t be deciphered without a key. Thomas decides to make a risky step: at night he deliberately lets the Griever to injure him to undergo Changing and receive access to his memories. If he is responsible for the Labyrinth, he should know how to escape it.
The Changing reveals that Thomas and Theresa are connected with the strange organisation named Creators - or, more specifically, its department called WICKED. Thomas tells to everyone what he knows now: the abyss under the Cliff is only a decoy - there is an exit to the outside world underneath. The words that are spelled by the Labyrinth are the code that will allow them escape. The code shall be entered to the computer on the other side of the “abyss”. Thomas and his friends prepare to escape the Glade. But Alby, who is just a cowardly remnant of who he was before his own Changing, tries to stop them. It’s time for Newt to step in again and replace the former leader, helping Thomas escape.
The Gladers attempt to run away at night. All the Grievers are attacking them now and their way is a constant battle - even those who were mere medics, cooks and farmers have to fight for their lives. When they reach the Cliff there are only twenty of them alive - less than a half. Thomas, Theresa and Chuck use the fight to jump from the Cliff and enter the code, opening a passage for the remnants of the Gladers.
They go through the long spiralling slide to the creepy underground bunker. Finally the Gladers see the Creators - the sick-looking adults, pale because of their underground life and dressed in the similar uniform. They observe the Gladers through the thick glass, making notes as if the teenagers were average lab rats. One of them, a woman in a business costume, greets the Gladers, saying that they did well and solved the puzzle. Another teenager is standing behind her. He is Gally. He recognizes Thomas, draws a knife and coldly throws it to his rival. Thomas would be dead if it wasn’t Chuck, stepping in front of him and taking the knife instead. Chuck collapses to the floor and dies in mere seconds.
Thomas is devastated. Chuck was someone resembling a younger brother to him and Thomas personally promised to return him home. Blinded by fury, he attacks Gally, beating him to half-death. The strange woman just doesn’t care....
Suddenly another armed group storms into the room and shoots the woman dead. They take the remaining Gladers with them, finally letting them see the outside world: dark and gloomy with heavy clouds and pouring rain. A big old bus is waiting for them. While they are inside, a horrible woman covered with scars grabs Thomas by hand and whispers him that he has been chosen to save the humanity from the Flare - an awful event of unknown nature that has already wiped out half of humanity. The Flare is a disease accompanied with actual solar flares that is a bit similar to radiation poisoning.
After a long drive the teenagers are accommodated in a strange army-style dormitory. Now they have real beds, real food and real blankets. The dormitory feels very safe in comparison with the Glade and the former Gladers finally allow themselves to relax and sleep.
But the epilogue reveals that they are not by any means safe. The last words of the story is the memo written by Ava Page - the WICKED manager - to her subordinates. She states that one of the groups has successfully passed the first level of trial and is transferred to the next one. The first level shall be filled with another experimental subjects.
The only good thing in the end is that the goal of all these atrocities is not as wicked as the organization’s name. The children are bred, selected, trained and tested to raise the ones who will indeed be able to stop the Flare and save humanity.