Unpredictability
Unpredictability plays a large role in Thomas's journeys with WICKED, especially after he escapes from WICKED. In The Scorch Trials, there are supposed to be no rules. However, in the same way that Thomas cannot predict what will happen in the world, so too can he never really know what WICKED is up to. For example, he only finds out partially about WICKED's mission, from the Rat Man's speech at the beginning of the story. Just as WICKED is unpredictable, so Thomas will also be forced to take unprecedented actions that he never would have thought of taking earlier. He must adapt to his environment and to whatever happens around him.
Fate
Just as Thomas' life is unpredictable, so too is it bound up with notions of fate. All of the subjects of WICKED are under the control of another organization: they do not really have free will. In The Scorch Trials, there are supposed to be no extra rules governing how the Gladers perform or act the Trials, but WICKED still has direct control over the subjects and some of the environment. Much of the Gladers' lives have been directed by someone else. Their lives have also been directed by an organization that has its own agenda, and this agenda does not have their best interests in mind. Still, fate continues to guide the Gladers along. The idea that things were meant to be a certain way continues to permeate the events that occur–after all, the Immunes end up in paradise at the end.
Gender Roles
The idea of gender roles is a theme in The Scorch Trials, in which many stereotypical gender roles are broken. Thomas's two closest female acquaintances are Teresa and Brenda, who are very capable and physically strong women. All of Group B is a formidable presence, especially when they capture Thomas and are supposedly going to kill him. Group B's leaders even remind Thomas that they solved the Maze faster than Group A did. While traditional gender roles are broken, the young, mostly teenage characters are also still learning who they are as people and as either a man or a woman.
Masculinity
Closely tied to the idea of gender roles in the stories, the main characters are young males who are still understanding their masculinity. Thomas and his best guy friends are figuring out what it means to be a man. Not normal teenagers, they have been forced to take on incredible physical and mental stress. They are also almost always part of a large pack of guys, and form sort of brotherhood as a result, even if there is some tension and competition within the group. The main antagonist, Janson, is also a male, but somehow he always feels "less" male than the toughened teenage boys. He is compared to a rat, the animal comparison effectively emasculating him, even in the face of his subjects.
Human Morality
Weighty questions concerning morality and experimentation surround every event of this story. WICKED is performing human experimentation, which is not ethical. However, they claim that the ends justify the means, and that they are doing it for a greater, moral good. Even at the end of the story, Thomas is still curious as to whether or not he should sacrifice himself to a moral cause and help save humanity. Thomas also really values human life, and so he always wonders whether killing people - even if it is killing to put someone out of suffering - is the right thing to do.
Desperation
Desperation and survival instinct are a huge force in the story. Thomas and his friends all have very strong senses of survival, knowing that they need to find a way to get by, day by day. However, beyond mere survival, desperation takes on a stronger note in this story. Thomas and his friends are not the only ones who are desperate: cranks are also desperate for some shred of hope - or a shred of food. WICKED is desperate to find a cure. Everyone is running on a timed clock, made worse by the current conditions of the world.
Normalness
Thomas and his friends just want everything to return to "normal." While Thomas understands that nothing can go back to normal - he cannot even remember his own memories from before WICKED swiped them - he and his friends yearn for some sort of stability and consistency. Many things fall apart in The Scorch Trials that can never return to their former states. These include Thomas's friendship with Teresa: Teresa had to make him feel utterly betrayed in order to save his life, and, as a human being, Thomas of course has difficulty trusting her again. Another difference is Thomas's friendship or engagement with Brenda, for whom he may or may not have feelings. Despite these permanent changes, much of the day-to-day survival that Thomas and his friends do is fueled by a desire to return to some balanced state of being.
