After escaping the maze the Gladers they Gladers live with WICKED but they are deserted. When they go through a hallway looking for Teresa the boys find a door labeled "Teresa". When they go in they find a boy named, Aris, who also lived in a maze but with all girls.
One day a man appears in the common room and tells the Gladers that they will have to go through the Scorch in two weeks and reach the safe haven. They are also told that they have a virus called the Flare and if they reach the safe haven they will get the cure.
While going through the Scorch the Gladers have to avoid the insane people called cranks who have the Flare. The Gladers meet people who are Cranks and have the Flare but are not insane yet, and their names are, Brenda and Jorge.
While going through the Scorch Tomas gets shot by a Crank. He is struggling to stay alive and on the journey he is taken by WICKED where they preform a surgery to fix the wound that turned out to be infected. Tomas later returns to his friends.
The Gladers meet the other group, group B, and Teresa is with them. They take Tomas and wanted to kill him but he convinces them to spare him. Teresa takes him into a cave where Aris is and together they push Tomas into the chamber that is in the cave.
Tomas finally gets out of the chamber, where Teresa and Aris wait for him. They explain to Thomas that they were forced to do put him into the chamber. Both the groups get to the safe haven and are taken away by WICKED.