Solving the Maze was supposed to be the end.
There are no rules. There is no help. You either make it or you die.
The Gladers have two weeks to cross through the Scorch—the most burned-out section of the world. And WICKED has made sure to adjust the variables and stack the odds against them.
Friendships will be tested. Loyalties will be broken. All bets are off.
There are others now. Their survival depends on the Gladers’ destruction—and they’re determined to survive.
The book starts in the middle of the night where Thomas wakes up and can't get back to sleep. He calls Teresa's name telepathically. After a while, Thomas finally falls asleep. Teresa calls out to him telepathically, but can't seem to get Thomas's attention. He wakes up to seeing everyone panicking about Cranks, which are people infected with the Flare, outside their windows. Thomas and the rest of the Gladers go around to investigate, finding that the room where they'd eaten pizza with the people who rescued them was locked. They ram the door down and turn on the lights to find the rescuers dead bodies hanging from the ceiling. They enter Teresa's room, which is empty, except for a boy that just came out of the bathroom named Aris, who's from Group B. He can also talk telepathically, and even had a telepathy partner named Rachel, but she was killed just like Gally had killed Chuck in the first book. Outside of the room is a plaque that says "Teresa Agnes. Group A, Subject A1. The Betrayer." An alarm, similar to the one in the Glade when the Box came up, goes off, and the room door locks until the alarm stops. Thomas opens the door to find no dead bodies. Even the plaque is changed to "Aris Jones, Group B, Subject B1. The Partner."
After they leave the room they find a man sitting in the middle of the room which they dub Rat Man. He tells them they are to make their way travel through the Scorch, a burned-out section of the land. And as an incentive, they've all caught the Flare and will receive a cure when they reach their destination. Shortly after he leaves, the Gladers discover tattoos on the back of their necks. Newt's says he's "The Glue". Minho's says "The Leader". Thomas' says 'To be killed by Group B". The Gladers enter a Flat Trans and wander through the darkness for about an hour when they hear strange whispers. Two boys get killed by molten steel balls that cover a person's head then decapitate them and roll away. Winston gets attacked too, but Thomas manages to save him. They enter the Scorch and eventually come to a building, where they heard screaming from a long way away. Teresa exits the building. Thomas senses a trap and approaches her. Teresa is crying, still telling him to get away from her. She kisses him and tells him to tell the Gladers to get as far away from her as possible.
Thomas and the Gladers hike towards a city to stock back up on supplies, along the way, he has another "memory dream" where Teresa and Thomas practice talking telepathically. A storm soon hits, killing off seven boys, including Winston. They stay inside a building when a Crank named Jorge welcomes them into the Crank House. Minho insults him and Jorge kicks him twice in a place where he was burnt from getting struck by lightning. Minho attacks Jorge and all the Cranks from upstairs come down. Fortunately, Thomas negotiates a deal with Jorge, keeping the Gladers from getting killed. Thomas meets Brenda, who becomes very forward when he first meets her. They go downstairs and eat, when the roof collapses, separating Thomas and Brenda from the others.
The two of them walk through the Underneath and fight some Cranks. Eventually, they make it onto the surface and sleep in a cab. Thomas wakes up from a nightmare and goes back to sleep. He has another dream memory where he and Teresa are listening in on a conversation between WICKED employees. Thomas wakes up again and sees words printed on a brick saying "Thomas, you're the real leader." They leave the car and are forced into a club by a few strangers. They dance to the music and are offered drinks that, of course, they're made to take too, making them feel dizzy. Brenda tries to kiss Thomas, but he says "You're not...her." and "You could never be her."
They wake up in a dark room with the three strangers who took them to the club. They are about to kill them when Minho and the other Gladers save them. While fleeing the strangers, a man that Thomas calls "Blondie" shoots Thomas in the left shoulder with a rusty bullet, giving him an infection. After the Gladers fail to heal Thomas, WICKED goes down and gets him in a machine called a Berg. While being healed, he overhears one the worker's conversations in which a woman stated that he wasn't supposed to get shot. He's taken back to where he came from, and he explains everything to the Gladers.
Later, Thomas hears Teresa's voice in his head, warning him that something terrible will happen, leaving him hurt and scared. And he had to trust her no matter what. She pauses and says that he won't hear from her for a while until they're back together. Newt and Thomas talk about how WICKED only made an exception for him and no one else. They see Teresa and Group B walking towards Group A with weapons. She hits Thomas multiple times with the butt of her spear for various reasons and takes him back to their base, getting dragged across the ground for hours. Thomas is fed once they get there and falls asleep, having another memory dream. The next morning the girls decided not to kill him. Thomas and the girls get about 7 miles away from the "Safe Haven" when Teresa motions for Thomas to follow her.
Aris appears and holds a knife to Thomas's back and leads him into a cave. Thomas sees a glowing green door, which he thinks could mean that there is a radioactive substance inside. Teresa reveals that she and Aris had a thing before and during the Maze and Scorch Trials, and had also manipulated Thomas to escape the Maze. They led him through the door, and into a gas chamber, but Thomas puts up one last fight, attacking Aris and Teresa, but fails. He gets dragged into the gas chamber and the gas released. Thomas passes out, feeling betrayed and sick from the gas and has another dream memory about being sent into the Swipe, then into the Maze. Thomas wakes up, and the gas chamber's door opens. Teresa apologizes, but Thomas still feels betrayed and cannot trust her. They run to catch up with the other group, as they only have a few hours until they must be at the Safe Haven. Teresa explains along the way that her telepathy with Thomas was "cut off" when WICKED came into her room and told her to tell Aris that they had to get Thomas to the point that he feels totally betrayed by them, and if they did anything against WICKED, Thomas dies. They kiss near a valley, but Thomas feels nothing.
They make it to the Safe Haven which turns out to be nothing more than a stick with a flag. While they discuss what to do now another storm builds up, and Bulb Monsters appear for the Gladers to fight. Only three people die during the fight. The Berg comes back and picks up the Gladers. A guard on it gets angry for them taking Jorge and Brenda with them, forcing Thomas to choose who to kill. He chooses Brenda, thinking it's a test, but he's wrong. He manages to keep both. They're fed and bathed and all fall asleep. Thomas has one more dream where Teresa speaks to him telepathically, saying things are about to get worse. He wakes up in a padded, white room. Teresa is telepathically speaking to him, saying the Flare was rooted too deeply in him, and they took him away. Thomas tells Teresa to go away. Teresa tells him WICKED is good and stops all telepathy connection for good.
- Thomas: a teenage boy who was a Runner in the Glade. He discovers he had some part in building WICKED and the Maze. He can speak telepathically with Aris and Teresa.
- Newt: the leader of the Gladers after the former leader dies in the first novel. He has a slight limp and is Thomas and Minho's best friend.
- Minho: the head Runner in the Glade. He is snarky and is a smart-aleck, which gets him in trouble frequently. He is best friends with Newt and Thomas.
- Brenda: a girl from Canada who has caught the Flare. She is not yet Gone, and leads Thomas and the Gladers through the Scorch. She is friends with Jorge. (It is later revealed that she is actually Immune)
- Aris: another boy who helped build WICKED; he spent the first trial with Group B. He can speak telepathically with Thomas and Teresa. He is Teresa's equivalent of Group B.
- Teresa Agnes: Thomas' best friend before the Glade; she can speak telepathically with Thomas and Aris. She spends much of the novel with Group B, whom she becomes the leader of. She is also under control of WICKED at times, which makes it difficult for Thomas to trust her.
- Jorge Gallaparga: a man who presents himself as the leader of the Cranks. He is close to Brenda.
- Sonya: Newt's equivalent of Group B.
- Harriet: Alby's equivalent of Group B.
- Rat Man: who is later revealed to be named Janson, a member of WICKED.
- Rachel: Thomas's equivalent of Group B.
- Frypan: The Cook for the Gladers in Group A.
- Winston: Keeper of the Slicers in the Glade.