After Thomas and the other Gladers escape from the Maze, they must now undergo more tests for WICKED. Thomas is a survivor of the Maze and he must now undergo more tests for WICKED or World In Catastrophe Killzone Experiment Department. The story begins with Thomas waking up with Theresa's voice in his head. He and the other Gladers are housed in a dormitory. During the night, Thomas and his closest friends, Minho and Newt, discover that the people that saved them from the Maze and put them in the dorms are now dead, hung. He and his friends explore the dorms, trying to find the other Gladers. They find a boy named Aris who claims to have escaped from a similar Maze experiment. Thomas is unable to find Theresa. He and his friends discover that they all have tattoos on themselves that designate their roles like leader, partner etc. Thomas discovers his role was "to be killed by Group B". He also discovers that Theresa's role is to be a betrayer.
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The Gladers finally meet one of the scientists behind WICKED. He tells them they must now go through phase two of the trials. The scientist explains that they are studying the Gladers and their response to various stimuli. The purpose of WICKED is to find a cure to the virus called the Flare, which is a degenerative disease that transforms a person into a crazed, cannibalistic monster. He mentions that they can actually even control what the Gladers see, feel and do, too. The Gladers are forced to undergo the Scorch trials or else be killed. The next day, they go through a trans portal and are chased out through a tunnel full of traps and into a desert.
The Gladers travel through the desert at night until they hear a girl screaming. The girl turns out to be Theresa who is wracked by some unknown secret. All she can tell Thomas is for him to get away from her. Thomas believes that Theresa was used as bait for some sort of trap and that she somehow resisted and saved him and the other Gladers. Thomas starts to regain some of his memories, some of which involve his relationship with Theresa. He remembers that he and Theresa were really close before the memories were taken away.
The Gladers travel towards a city. In the city, they encounter a man infected with the Flare, who acts crazy. A storm wracks the city, lightning striking fires everywhere. After the storm, they meet a Crank named Jorge who claims to be the leader of the Cranks in the building. After an altercation, Thomas and Jorge find themselves on equal grounds. Thomas asks Jorge to help him and in exchange he will make sure Jorge gets his hands on the Cure, if they find it. Jorge introduces the group to his trusted partner, Brenda, another teenage girl. They agree they will help deliver the Gladers to WICKED in exchange for the cure.
Together the group travel through the city, having to face Cranks who try to attack them along the way. Thomas finds a message on a wall that says that he is the real leader. He later finds his name all over the city. He and his group are captured by another group of Cranks who drug them. They are eventually saved by Minho. Later on, WICKED attacks the group and take Thomas away, with Brenda likely being complicit in the operation. In his half-dream state, Thomas learns that he is very important to WICKED. Thomas is returned to the Gladers healed and safe, with questions running through his head. Thomas receives a telepathic warning from Theresa saying that something terrible is going to happen to him soon.
As the Gladers travel further into the desert, they encounter Theresa and a group of girls. Theresa is unfriendly and nasty and plans on killing Thomas for something he did to her which he has no idea of. Theresa plan on following her orders from WICKED. During the night, Thomas convinces another girl to mutiny against Theresa so that all the survivors can join force and work together against WICKED. Thomas learns from the other girls that Theresa was pretending all along to get close to Thomas, that in reality, she hates Thomas. As the rest of the group travels, Theresa makes an appearance and tells Thomas "the act is over". She appears with Aris, and kisses Aris, crushing Thomas who had a sort of romantic relationship with Theresa in the previous book. Then, they shut Thomas up in a room, leaving him to die.
Thomas thinks he is dead, but he is soon rescued by Theresa and Aris again. They claim that what happened before was all an act that WICKED forced them to do to save Thomas' life. But it is too late for Thomas as things are irreparably changed between him and Theresa.
Eventually he and the Gladers will make it to the Safe Haven where they are attacked again by a WICKED monster. They learn that even though they succeeded in the Scorch trials, things are still going to get a lot worse.
Best part of story, including ending:
I didn't like that by the end of the story there were still so many unanswered questions and even more torture for the poor kids in store.
Best scene in story:
My favourite scene is when Minho rescues Thomas and Brenda from some Cranks because it was heart-warming that Minho put himself in such a dangerous situation to save Thomas.
Opinion about the main character:
I like that Thomas is a good leader but this time, I felt sorry for Thomas because all the variables in the trials were messing him up permanently.