When Thomas, Minho, Frypan, Winstons and Newt escaped from the Maze they were welcomed by Mr. Janson into the facility they were held captives now. This protected facility made them believe they were safe, but nothing more away from the truth. When Thomas decides to investigate further about the facility they were in, he finds out that everything is just a scam.
Now they have to escape from there, where they induced all the young souls into a state of incubation where the WCKD would experiment with them using them as guinea pigs. They succeded in escaping this facility, but now the WCKD is after them, they will have to run for their lives while some of them will not last long. Now they have to find safe places and there’s a group hidden in the mountains that seems like a great opportunity to find out what’s really going on, but things get a little fuzzy.