The Scorch Trials and its narrative follows immediately after the first book in the series, The Maze Runner. There a group of a few dozen teenage boys were apparently held captive in a compound bounded by an enormous maze. At the end of The Maze Runner, the boys, under the leadership of Thomas, finally escape the maze and its tortures. They were determined to face their captors only to be whisked away to safety by what they thought was a group of liberators. In The Scorch Trials, we find out that the liberators were just another fold in the schemes by the same group that had delivered them to the maze in the first place. Once again the group find themselves in danger, but they have learned more about what is going on and what is at stake.
A government group called WICKED is apparently running this show. Due to an extended period of radical sun flares, much of the Earth has become little more than harsh desert and a sizable fraction of the planet's population has died. Of the surviving fraction, a great number have been inflicted with some sort of disease called "the flare" that might just wipe out the remainder. It seems that WICKED was put together by the surviving governments to find the cure to this flare. How the attempts at finding the cure are connected to what the boys have been put through is not clear. It just seems a sadistic plot by unseen forces to torture a group of youngsters. What makes things all the more confusing for them, is that despite everything that they are going through, every now and then they receive some hint that they were initially willing participants in the schemes of WICKED. However, with their memories erased, they feel like victims.
In The Scorch Trials the boys are put through further tests where they must make their way across 100 miles of desert wasteland to what has been called a "safe haven". However, each leg of the journey is full of tests and enemies, including a second all-girl team of survivors from a separate maze system. Apparently WICKED has put them in direct competition in a survival of the fittest test. As the story ends, all of the survivors are rescued and led to believe that WICKED has learned what it needed to learn. However, that certainly is not the case for Thomas who finds himself betrayed once again. I now move onto the third part of the story, The Death Cure.