Originally the studio had a "wait-and-see" policy for greenlighting this sequel depending on how the first movie did. However, they decided two weeks before the premier of the first movie to go ahead and greenlight The Scorch Trials anyway as the publicity and reviews were overwhelmingly good.
The plot, facts and characters from the movie are wildly different than from the book, including the story arc, the flare and character backstory and development.
According to the commentary on the deleted campfire scene between Thomas (Dylan O'Brien) and Newt (Thomas Brodie-Sangster), Thomas Brodie-Sangster came up with a line about how Thomas is the reason they're free and how they all have their roles to play, and even in The Glade he'd been told that he was The Glue that held everyone together, which is tattooed on his neck in the book, but not in the movie.
Three actors from this movie - Thomas Brodie-Sangster, Aidan Gillen, and Nathalie Emmanuel - appeared in Le Trône de fer (2011) but did not meet until filming The Scorch Trials.
The way the Gladers escaped WICKED headquarters was very different from the book. In the book, they went through a Flat Trans and must walk through a very dark tunnel with silver goops attacking their faces. In the movie, this never happened.