Before the maze and before WICKED there was the flares. The sun has scorched the earth leaving people either dead or infected with madness. Those who are infected will eventually die. Some have survived the madness, but one day the bergs come. The people on the bergs shoot darts with a virus that will kill the remaining people. Many people die with in a day or two of being shot by the darts. Mark, Alec, Trina, Lana, and a few other people make it out of their village alive. Mark and Alec take down a berg, and via a pad they find out where the bergs are coming from. They decide to make their way to the berg home base. They come across another village where in the middle of all the corpses is a little girl, who appears to be immune to the virus. As they make camp in the forest, Mark and Alec scout ahead and come into contact with a group of survivors from the little girl's village. They are captured when their fate is about to be decided more darts fly through the air killing most of group. There is also a forest fire, which forces Trina, Lana, and the little girl to flee. Mark and Alec track them to the berg command center, fearing that they have been captured. They get trapped on a berg where they discover what the Post-Flares Coalition has in store for the rest of the human population.
I'm glad James Dashner did a prequel to the Maze Runner series. There were a few questions going through my head when I was reading Maze Runner and the other two books. The Kill Order gives you insight into what the world was like before WICKED formed, and before Thomas when into the maze. It also introduces us to the virus that would become the Flare. If you are a fan of the Maze Runner series this is a must read.