Book Summary (Spoilers)
The book starts with Thomas and the other teenagers known as the "Gladers", who had escaped from an experiment known as The Maze in the previous book, sleeping in the dormitory they were brought to by a group of rescuers. Thomas is woken by a telepathic communication with Teresa, the only female Glader, who placed in another room. She says "Tom, something's wrong" and then the telepathic communication is cut off.
As he wakes up, he finds that the facility is being attacked by Cranks, aggressive zombie-like people whose brains have been affected by a plague known as "The Flare". He and other Gladers escape into the facility's common area before the Cranks manage to get in, and discover that their rescuers are dead. They enter a room which says "Teresa Agnes. Group A, Subject A1. The Betrayer", but find that Teresa is missing from her room, and in her place is a boy named Aris. Thomas attempts to find Teresa, but there are no other rooms, which makes him wonder where the food had came in the previous night, but he realizes the details of the previous day have grown fuzzy in his head. He checks to make sure that Teresa is not among the dead bodies, and defeatedly returns to the Gladers. The Gladers are initially suspicious of Aris, but they find out that he had escaped from a similar Maze experiment, where he was the only male in a group of girls. Aris reveals he can communicate telepathically with Thomas, but that his telepathic partner, Rachel, was killed in the escape by a girl named Beth, similarly to how Chuck was stabbed by Gally. This leads Thomas to wonder if he was supposed to be killed, instead of Chuck.
The Gladers discover a tattoo on Aris's neck that says "Property of WICKED. Group B, Subject B1. The Partner." They discover that they all have similar tattoos, but only some of them have special designations like Aris does. Minho is "The Leader", Newt is "The Glue", while Thomas is "To be killed by Group B", which worsens his suspicion that he was to be killed by Gally. The Gladers realise that their escape from WICKED was a farce, another "Variable". An alarm goes off, and the Gladers re-enter the common area to find out the bodies have disappeared. The beds in their dorm have been re-made, and the Cranks have disappeared, brick walls erected outside the window. The sign outside Teresa's room has been changed to "Aris Jones. Group B, Subject B1."
Thomas attempts to contact Teresa telepathically again and succeeds, but Teresa warns him not to talk to her in her head, leading him to suspect if her memories have been wiped again. He tries, despite her warning, but the telepathy is cut off again. They're left hungry for three days, during which Thomas has "memory dreams", where he remembers snippets of his past. Food magically appears in the common area after three days. The Gladers also find an oddly dressed man, whom Minho dubs as 'Rat Man'. Thomas attempts to approach him, but meets an invisible wall, and Rat Man tells him to wait for forty-seven minutes. Forty-seven minutes later, Rat Man reveals to them that the hanging bodies of the rescuers and the brick walls were a demonstration to show the Gladers that WICKED could manipulate their nerve recepticles. He tells them they're part of an experiment, and that they're playing their part in 'saving the human race'. He tells them that a 'Flat Trans' will appear in the common area the next day at 6 in the morning, and will close five minutes later. In order to pass the Scorch trials, the Gladers must move through the Flat Trans, find open air, and move a hundred miles North and find a place called Safe Haven within two weeks. He claims that the Gladers have all caught the Flare, and that they will need to pass the Scorch Trials to obtain the cure.
The next day, the Gladers pass through the Flat Trans and find themselves in a tunnel filled with traps - a head-eating silver ball attacks three Gladers and kills two, but Thomas is able to save Winston before it kills him. The Gladers exit the tunnel and find themselves in the middle of a vast desert known as the Scorch, and they can see a city in the distance. They travel through the Scorch and encounter two Cranks, who tell them some facts about the Flare before disappearing. On their way, they encounter a tower from which a girl's screams can be heard, and the Gladers recognize it as the screams from the Changing. The screams are abruptly cut off when the Gladers near the tower, and a girl exits it. Thomas approaches her in the hope that it is Teresa, although he senses a trap when he approaches her. When he enters the tower, Teresa is crying, and under the control of WICKED. She breaks away from WICKED's control to kiss Thomas and warns him of the trap. Thomas runs from the tower and informs his friends of the trap, telling them to run away. He darts off, refusing to answer any of their questions.
A few hours later, he stops, and the Gladers catch up with him. Minho questions him, and Thomas tells him about how Teresa was behaving like Gally and Alby, under the control of WICKED. He reveals his fear that WICKED will punish her for having warned him about the trap, but Minho manages to allay his fears. They rest for a while, and Thomas has another "memory dream" of Teresa and him practizing their telepathy. A storm brews up, and they find an old man, who warns them that there are "bad people" in the city. They run towards the city, anyway, to obtain supplies and shelter. Lightning strikes kill attacks eight Gladers, but Thomas is able to save Minho, who isn't "too badly injured". They reach the city and take refuge in the nearest building. When they wake up, they encounter a man named Jorge who claims to be a Crank. Minho attacks him, and the Gladers are confronted with an army of Cranks with weapons. Thomas is able to strike a deal with Jorge to help the Gladers reach safe haven in exchange for obtaining the cure. Jorge and a teenage girl named Brenda help them escape, but an explosion separates Thomas and Brenda from the rest of the group. Brenda thinks that the rest of the Cranks were the ones who rigged the explosion to try and kill them. Brenda leads Thomas into a series of underground tunnels called "The Underneath", where they are confronted by a group of Gone Cranks. Thomas kills one of the Cranks, and they manage to escape from the Underneath. They find an abandoned truck where they hide for the night, and Thomas finds a sign that says "Thomas, you're the real leader." Brenda tells him that the signs are all over the city, and apologises for not telling him earlier.
They are kidnapped by a group of Cranks who force them into a party and drug them. Brenda tries to kiss Thomas before passing out, but Thomas refuses her advances due to his feelings for Teresa. When they wake up, they're both tied up, and Brenda's gagged. The Cranks ask Thomas to explain where he came from and the presence of the signs about him all over the city. They are rescued by the rest of the Gladers and Jorge, who have the Cranks in hostage. Brenda behaves coldly with Thomas, presumably because he rejected her advances towards him. They escape, but Thomas is shot in the shoulder by one of the Cranks with a rusty bullet, leading to an infection. Minho attacks the shooter, and Jorge is able to get the bullet out of him, but the infection worsens, and Thomas has to be carried by his friends.
WICKED captures Thomas to heal him, and at WICKED's Compound, Thomas overhears conversations between people, saying that the bullet wasn't supposed to be part of the trials, that he's among WICKED's top "candidates", and they can't let him die. He is returned to the Gladers, and explains everything he overheard there. The Gladers are surprised that WICKED went so far to save Thomas, when so many people had died in the trials earlier. He later receives a telepathic message from Teresa, warning him that something awful is going to happen to him, and he needs to trust her no matter what happens.
The Gladers are ambushed by Group B, which now led by Teresa. Group B takes Thomas as prisoner, and Teresa repeatedly hurts him with the butt of her spear. One of the girls, Harriet, reveals their plans to kill him, and they drag him to their camp and tie him up. Teresa repeatedly whispers to him to trust her, but Thomas finds it hard to listen to her advice. He learns that the girls have been given the mission of killing him, and they have been given much better supplies than the Gladers had been. Teresa repeatedly talks about "what Thomas did to her", which makes Thomas wonder if her memories have been manipulated. Thomas convinces the girls to spare him, resulting in Teresa leaving them. Some of the other girls tell Thomas that Teresa had never liked him and their earlier kiss had been forced upon her by WICKED. They also tell him that they had been given very specific instructions on killing him, and that Teresa has probably left for the cave they're supposed to kill him at. They let him eat with them and they move towards safe haven.
On the way, Thomas encounters Teresa, who tells him to follow her. None of the other girls seem to notice her, which makes Thomas suspicious. Teresa leads Thomas into a cave, and Aris joins them. Teresa claims that she had been manipulating Thomas all along, and that she had always known and loved Aris. Teresa kisses Aris on the cheek, and she says that WICKED made her choose between killing Thomas and letting herself and Aris die, and they push him into a gas chamber. Thomas asks Aris, "What did Rachel look like as she bled to death?" Aris is caught off-guard, and Thomas attempts to escape, but Teresa concusses him with a spear and throws him into the gas chamber.
Thomas sees another memory dream of his relationship with Teresa before the Maze, confusing him further about Teresa's intentions. The room is gassed, and Thomas passes out. When he wakes up, his scars are healed and he exits the gas chamber. Teresa runs to him, crying, apologizing, and explains to him that she was forced to do it against her will, that the betrayal was all an act, and that WICKED had threatened to kill Thomas if she would not do that. Teresa explains everything as they move towards safe haven, and tries her best to amend their relationship, but Thomas is still afraid to trust her. Teresa kisses him near a valley, but Thomas "feels nothing".
The Gladers and Group B make it to the location where the safe haven is supposed to be, but they encounter a storm and are attacked by "bulb monsters", another biotech creation of WICKED. Teresa hands Thomas a weapon, and the Gladers and Group B manage to kill off the bulb monsters. A WICKED Berg arrives and they make their way on board. Thomas falls multiple times, but Teresa saves him. WICKED will only allow one of Jorge and Brenda to come with them. Thomas chooses Jorge, thinking it's still a trial, but it turns out that it's not. Thomas overpowers the guard while Teresa rescues Brenda. Thomas forces the guard at gunpoint to allow both of them to stay. The guard agrees, telling them that this had been their actual test.
Later, Brenda communicates telepathically with Thomas while he's dreaming, and warns him that things are going to get bad for him. Thomas realises that Brenda had been working for WICKED all along.
Thomas wakes up in a white room, and attempts to contact Teresa, but the telepathy is cut off. Teresa later manages to contact him, telling him that the others are being told that he has succumbed to The Flare. Thomas doesn't trust her, and tells her to go away, and to tell WICKED to go away too. Teresa reluctantly agrees, but reminds him that "WICKED is good".
As he wakes up, he finds that the facility is being attacked by Cranks, aggressive zombie-like people whose brains have been affected by a plague known as "The Flare". He and other Gladers escape into the facility's common area before the Cranks manage to get in, and discover that their rescuers are dead. They enter a room which says "Teresa Agnes. Group A, Subject A1. The Betrayer", but find that Teresa is missing from her room, and in her place is a boy named Aris. Thomas attempts to find Teresa, but there are no other rooms, which makes him wonder where the food had came in the previous night, but he realizes the details of the previous day have grown fuzzy in his head. He checks to make sure that Teresa is not among the dead bodies, and defeatedly returns to the Gladers. The Gladers are initially suspicious of Aris, but they find out that he had escaped from a similar Maze experiment, where he was the only male in a group of girls. Aris reveals he can communicate telepathically with Thomas, but that his telepathic partner, Rachel, was killed in the escape by a girl named Beth, similarly to how Chuck was stabbed by Gally. This leads Thomas to wonder if he was supposed to be killed, instead of Chuck.
The Gladers discover a tattoo on Aris's neck that says "Property of WICKED. Group B, Subject B1. The Partner." They discover that they all have similar tattoos, but only some of them have special designations like Aris does. Minho is "The Leader", Newt is "The Glue", while Thomas is "To be killed by Group B", which worsens his suspicion that he was to be killed by Gally. The Gladers realise that their escape from WICKED was a farce, another "Variable". An alarm goes off, and the Gladers re-enter the common area to find out the bodies have disappeared. The beds in their dorm have been re-made, and the Cranks have disappeared, brick walls erected outside the window. The sign outside Teresa's room has been changed to "Aris Jones. Group B, Subject B1."
Thomas attempts to contact Teresa telepathically again and succeeds, but Teresa warns him not to talk to her in her head, leading him to suspect if her memories have been wiped again. He tries, despite her warning, but the telepathy is cut off again. They're left hungry for three days, during which Thomas has "memory dreams", where he remembers snippets of his past. Food magically appears in the common area after three days. The Gladers also find an oddly dressed man, whom Minho dubs as 'Rat Man'. Thomas attempts to approach him, but meets an invisible wall, and Rat Man tells him to wait for forty-seven minutes. Forty-seven minutes later, Rat Man reveals to them that the hanging bodies of the rescuers and the brick walls were a demonstration to show the Gladers that WICKED could manipulate their nerve recepticles. He tells them they're part of an experiment, and that they're playing their part in 'saving the human race'. He tells them that a 'Flat Trans' will appear in the common area the next day at 6 in the morning, and will close five minutes later. In order to pass the Scorch trials, the Gladers must move through the Flat Trans, find open air, and move a hundred miles North and find a place called Safe Haven within two weeks. He claims that the Gladers have all caught the Flare, and that they will need to pass the Scorch Trials to obtain the cure.
The next day, the Gladers pass through the Flat Trans and find themselves in a tunnel filled with traps - a head-eating silver ball attacks three Gladers and kills two, but Thomas is able to save Winston before it kills him. The Gladers exit the tunnel and find themselves in the middle of a vast desert known as the Scorch, and they can see a city in the distance. They travel through the Scorch and encounter two Cranks, who tell them some facts about the Flare before disappearing. On their way, they encounter a tower from which a girl's screams can be heard, and the Gladers recognize it as the screams from the Changing. The screams are abruptly cut off when the Gladers near the tower, and a girl exits it. Thomas approaches her in the hope that it is Teresa, although he senses a trap when he approaches her. When he enters the tower, Teresa is crying, and under the control of WICKED. She breaks away from WICKED's control to kiss Thomas and warns him of the trap. Thomas runs from the tower and informs his friends of the trap, telling them to run away. He darts off, refusing to answer any of their questions.
A few hours later, he stops, and the Gladers catch up with him. Minho questions him, and Thomas tells him about how Teresa was behaving like Gally and Alby, under the control of WICKED. He reveals his fear that WICKED will punish her for having warned him about the trap, but Minho manages to allay his fears. They rest for a while, and Thomas has another "memory dream" of Teresa and him practizing their telepathy. A storm brews up, and they find an old man, who warns them that there are "bad people" in the city. They run towards the city, anyway, to obtain supplies and shelter. Lightning strikes kill attacks eight Gladers, but Thomas is able to save Minho, who isn't "too badly injured". They reach the city and take refuge in the nearest building. When they wake up, they encounter a man named Jorge who claims to be a Crank. Minho attacks him, and the Gladers are confronted with an army of Cranks with weapons. Thomas is able to strike a deal with Jorge to help the Gladers reach safe haven in exchange for obtaining the cure. Jorge and a teenage girl named Brenda help them escape, but an explosion separates Thomas and Brenda from the rest of the group. Brenda thinks that the rest of the Cranks were the ones who rigged the explosion to try and kill them. Brenda leads Thomas into a series of underground tunnels called "The Underneath", where they are confronted by a group of Gone Cranks. Thomas kills one of the Cranks, and they manage to escape from the Underneath. They find an abandoned truck where they hide for the night, and Thomas finds a sign that says "Thomas, you're the real leader." Brenda tells him that the signs are all over the city, and apologises for not telling him earlier.
They are kidnapped by a group of Cranks who force them into a party and drug them. Brenda tries to kiss Thomas before passing out, but Thomas refuses her advances due to his feelings for Teresa. When they wake up, they're both tied up, and Brenda's gagged. The Cranks ask Thomas to explain where he came from and the presence of the signs about him all over the city. They are rescued by the rest of the Gladers and Jorge, who have the Cranks in hostage. Brenda behaves coldly with Thomas, presumably because he rejected her advances towards him. They escape, but Thomas is shot in the shoulder by one of the Cranks with a rusty bullet, leading to an infection. Minho attacks the shooter, and Jorge is able to get the bullet out of him, but the infection worsens, and Thomas has to be carried by his friends.
WICKED captures Thomas to heal him, and at WICKED's Compound, Thomas overhears conversations between people, saying that the bullet wasn't supposed to be part of the trials, that he's among WICKED's top "candidates", and they can't let him die. He is returned to the Gladers, and explains everything he overheard there. The Gladers are surprised that WICKED went so far to save Thomas, when so many people had died in the trials earlier. He later receives a telepathic message from Teresa, warning him that something awful is going to happen to him, and he needs to trust her no matter what happens.
The Gladers are ambushed by Group B, which now led by Teresa. Group B takes Thomas as prisoner, and Teresa repeatedly hurts him with the butt of her spear. One of the girls, Harriet, reveals their plans to kill him, and they drag him to their camp and tie him up. Teresa repeatedly whispers to him to trust her, but Thomas finds it hard to listen to her advice. He learns that the girls have been given the mission of killing him, and they have been given much better supplies than the Gladers had been. Teresa repeatedly talks about "what Thomas did to her", which makes Thomas wonder if her memories have been manipulated. Thomas convinces the girls to spare him, resulting in Teresa leaving them. Some of the other girls tell Thomas that Teresa had never liked him and their earlier kiss had been forced upon her by WICKED. They also tell him that they had been given very specific instructions on killing him, and that Teresa has probably left for the cave they're supposed to kill him at. They let him eat with them and they move towards safe haven.
On the way, Thomas encounters Teresa, who tells him to follow her. None of the other girls seem to notice her, which makes Thomas suspicious. Teresa leads Thomas into a cave, and Aris joins them. Teresa claims that she had been manipulating Thomas all along, and that she had always known and loved Aris. Teresa kisses Aris on the cheek, and she says that WICKED made her choose between killing Thomas and letting herself and Aris die, and they push him into a gas chamber. Thomas asks Aris, "What did Rachel look like as she bled to death?" Aris is caught off-guard, and Thomas attempts to escape, but Teresa concusses him with a spear and throws him into the gas chamber.
Thomas sees another memory dream of his relationship with Teresa before the Maze, confusing him further about Teresa's intentions. The room is gassed, and Thomas passes out. When he wakes up, his scars are healed and he exits the gas chamber. Teresa runs to him, crying, apologizing, and explains to him that she was forced to do it against her will, that the betrayal was all an act, and that WICKED had threatened to kill Thomas if she would not do that. Teresa explains everything as they move towards safe haven, and tries her best to amend their relationship, but Thomas is still afraid to trust her. Teresa kisses him near a valley, but Thomas "feels nothing".
The Gladers and Group B make it to the location where the safe haven is supposed to be, but they encounter a storm and are attacked by "bulb monsters", another biotech creation of WICKED. Teresa hands Thomas a weapon, and the Gladers and Group B manage to kill off the bulb monsters. A WICKED Berg arrives and they make their way on board. Thomas falls multiple times, but Teresa saves him. WICKED will only allow one of Jorge and Brenda to come with them. Thomas chooses Jorge, thinking it's still a trial, but it turns out that it's not. Thomas overpowers the guard while Teresa rescues Brenda. Thomas forces the guard at gunpoint to allow both of them to stay. The guard agrees, telling them that this had been their actual test.
Later, Brenda communicates telepathically with Thomas while he's dreaming, and warns him that things are going to get bad for him. Thomas realises that Brenda had been working for WICKED all along.
Thomas wakes up in a white room, and attempts to contact Teresa, but the telepathy is cut off. Teresa later manages to contact him, telling him that the others are being told that he has succumbed to The Flare. Thomas doesn't trust her, and tells her to go away, and to tell WICKED to go away too. Teresa reluctantly agrees, but reminds him that "WICKED is good".