Why do signs around the city proclaim Thomas as the real leader, while Minho's neck tattoo labels Minho as the leader of the group? Who is the real leader, and why is this important?
Both Thomas and Minho are leaders in their own right; they are different types of leaders. In the end, Thomas is understood by WICKED to be the "real" leader: he is a better overall leader, because he is not as rash or impulsive or aggressive as Minho. However, Minho's style of leadership does get the Gladers through the first part of the Scorch effectively. Leadership is particularly important in this second part of the Trials, because, as WICKED tells the boys, there are no rules here. Now they must figure out their own organization, hierarchy, and responsibilities. The Gladers will need leaders like Thomas and Minho in order to get them through the Scorch as best as possible.
What is the importance of the environment of the Scorch in terms of the overall story?
The environment of the Scorch is the literal, physical setting, and is as much of a trial for the Gladers as the various weapons, tricks, and monsters that appear in the Trials are. The Scorch is heated and stifling, reflecting the earlier horror of the sun flares that decimated the earth. It also reflects the terrible heat of the boys' mission: they have to reach the cure and Safe Haven before their time is up. The natural dangers of the Scorch include the heat and sunburn, as well as terrifying lightning storms. The Scorch reflects the worst-burned part of the earth; it demonstrates just how cruel and indifferent and dangerous nature can be.
How does Teresa's betrayal of Thomas affect their friendship?
Teresa has to betray Thomas in order to appease WICKED. WICKED needs this in order to find out how the feeling of betrayal affects Thomas's mind: the organization wants to use this to find their cure. However, WICKED does this in a horrible way when looking at it from a human perspective. Teresa and Thomas are best friends, and this incident forever scars their friendship. Immediately afterwards, Teresa attempts to explain that she did this not only in order to appease WICKED, but also to save Thomas's life. However, Thomas is already too hurt to ever trust Teresa fully again. This shows that, although experiments can be done to test hypotheses, human subjects are more complicated than simple 'experiment subjects'.
What role does Aris play in Thomas and Teresa's relationship?
Aris is a new character in the Scorch Trials. He is a link to Thomas's past, and plays a vital role in driving a wedge between Thomas and his best friend Teresa. Aris is able to do this because he is also able to speak to Teresa and Thomas telepathically, and also because, in flashbacks, it seems that he was another helper in creating the Maze. Aris's function as Teresa's counterpart in Group B - even speaking to her during the Maze - reminds Thomas that there are other people out there, and that perhaps he and Teresa (and their friendship) are not as unique and important as he previously thought.
What is the symbolic significance of the Underneath that exists under the city of the Scorch?
Brenda attempts to take Thomas through a series of underground passages to go through the city of the Scorch in a faster manner. However, they are attacked by very Gone, terrifying Cranks underground, and Thomas insists that they travel aboveground. In many ways, the Underneath is symbolic of the hidden terrors that the earth now has to offer. For example, the Flare is originally "hidden" in people's bodies, and people do not know that they are infected until the symptoms of madness and bleeding occur. The Underneath symbolizes the unknown, and at this point in the story, Thomas and his friends are still "in the dark" about what is going on in the world, and why WICKED is doing all of these terrible things to them.
How does the labeling of the Gladers by their neck tattoos affect them as they move towards the Safe Haven?
WICKED has labeled the Gladers with neck tattoos, and these labels give them designated roles to play in the Scorch Trials. While the boys do not initially believe in the importance or significance of these tattoos, they slowly accept these roles and play them out in the Scorch. These tattoos are a reminder of how the boys' destinies have largely been predetermined for them by WICKED, at least up to this point in their lives. Even if they did not originally believe in their roles, or want to play those roles, the boys are being manipulated, used, and led around by a larger force: the organization of WICKED.
Why does the Rat Man tell the Gladers that they have the Flare? How does it affect them, along with the situation around them?
The Rat Man's revelation to the Gladers that they are infected is meant to propel them faster towards the Safe Haven. His words are a reminder that all human beings have to work towards something. This is also important because, up until this point, Thomas and his friends were not really sure why they were doing all the things they were doing for WICKED. Now, suddenly, they have something they have to work towards that has relevance to their individual selves. None of them wants to die, so of course they will work as hard as possible towards the cure. This is a reminder of how selfish human beings can be, and that perhaps WICKED's purpose of helping "save the world" may not be the purest goal.
Why do the Gladers have to go through a tunnel to reach the Scorch? How does the tunnel affect them?
The Gladers walk through a Flat Trans in the WICKED facilities to reach the Scorch. This tunnel signifies how Thomas and his friends are "kept in darkness" about where they are going, much as they are "kept in the darkness" about the meaning of all the Trials that they have been forced to undergo. This tunnel also has terrible slicing weapons inside of it, revealing how helpless Thomas and his friends really are. Just like they are trapped in the tunnel, so too are they trapped in WICKED's experiment, until they can reach an open space.
What kind of place is the "Safe Haven," and how is that significant with respect to the overall narrative?
The Safe Haven ends up being just a literal stick in the sand. Its simplicity and clear lack of safety - monsters come out and attack Thomas and his friends shortly afterwards - are anything but a "Safe Haven." It is another reminder of how WICKED's words cannot be trusted. At the same time, it is testament to how the Rat Man told the Gladers not to trust their senses. At first glance, no cure exists at the Safe Haven, but perhaps all of the torture that the Gladers have just undergone is a contribution to a cure that will eventually be "at the end" of what they are reaching for. The Safe Haven at the end of the Scorch makes sure to leave the Gladers high and dry so that they are fully at the mercy of WICKED.