It's pretty safe to say that darkness pretty often means something bad when it comes to books and movies. When it's dark out, that's when the monsters and demons come out to play.
We encounter a lot of darkness in The Scorch Trials, and it really messes with the Gladers' emotions. When they're first faced with pitch black, for example, the spooky-scary feeling sets in right away: "Newt stood quietly, staring at that long, narrow gap of blackness as if he expected demons from the underworld to come flying through" (3.31).
Darkness can unnerve people, just as it does Newt. And he has pretty good reason to be scared, because when the kids flick the lights on, they find a bunch of dead bodies hang from the ceiling. Hey, sometimes it's better not to see what's lurking in the darkness.
In the Flat Trans, darkness immediately envelops the Gladers, who desperately want light. It's a terrifying situation: nobody can tell what's going on, and danger is sure to be lurking around every corner. But when the kids finally do see light, the transition is simply too much: "After so long in pitch darkness, the sudden appearance of light overpowered him"(15.40).
Ugh, first these kids want light, and then they can't handle the light when they get it. Not only does darkness mess with the emotions of many of the characters, but it also physically damages their eyes. It's bad news, either way.
Little by little, the darkness takes its toll, until it just becomes too much. After a certain point, in fact, Thomas just decides he can't bear traveling anymore: "He'd had enough of long black tunnels. Enough to last a lifetime. 'I want daylight. I don't care what it takes. I want daylight. Now'" (34.9).
Being restricted from seeing can really mess with you; not only can you not see, but you start to feel nervous. This seemingly never-ending darkness just adds to the suspense that keeps building in The Scorch Trials.
Of course, the darkness also symbolizes the fact that the Gladers really have no idea who they are or what they are doing in the Scorch Trials. Their memories have been wiped; they're being manipulated at all times; and nothing they see can be trusted. They're truly being kept "in the dark" about just about everything.