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The Kill Order serves as the prequel to James Dashner'sMaze Runner trilogy and chronicles how the dystopian Earth of the series came to be. The novel was published August 1, 2012 by Delacorte Press, an imprint of Random House. The trilogy is currently being shopped as a possible film series.

Plot Summary
The story opens with a prologue of Teresa and Thomas preparing to enter the maze. The actual story begins, however, thirteen years earlier, with Mark, one of the novel's protagonists, waking up in a North Carolinian refugee camp. After going through the typical morning routines, he and the rest of his group of survivors hear the sound of an engine in the sky. Everyone throughout the settlement is shocked by the sound because they thought that the few Bergs that existed only went to Asheville, a large, government-funded refugee camp 60 miles away. They gather in the town center to figure out why the ship has arrived. But as the doors open, people with bio-hazard suits emerge and being to shoot into the crowd with darts. Everyone starts running but in the chaos, Darnell (one of Mark's friends) is shot. Alec, the leader of Mark's group and a former sergeant in the Army, recruits Mark to help him put an end to the shooting. They are successful and as the Berg retreats, Mark and Alec stow away on the ship. As Alec breaks down the door to the rest of the ship, Mark looks around the Berg for any weapons and discovers in one corner a box of darts that have a large label on them, warning that they contain a highly contagious pathogen. After Alec breaks down the door, they enter the main part of the ship. As they attempt to interrogate the few crew members on board about why their settlement was attacked, the pilot downs the Berg. After getting free of the wreckage, Alec and Mark decide to head back to their camp, fearing that those darts had infected their home. Sure enough, as they approach the settlement, they smell corpses and discover the streets to be eerily abandoned. They hear a scream and head toward the sound to discover the other members of their group around the door to a building. Darnell is inside and was the one who had been the source of the inhuman scream that had brought them to that building in the first place. Darnell then commits suicide in order to end the intense pain in his head. Alec then tells the entire group that he was able to determine the Berg's base from a work pad he found in the wreckage. As they're packing, Misty, another member of their group, complains of a headache and they all know that this means she's sick too. They quarantine her but all leave in search of answers except for Misty's best friend, Toad. However, as they camp out the first night, Toad finds them and yells at them for abandoning him, revealing in the process that Misty has already died and that he now is infected as well. After Toad gets aggressive with the group,Alec pulls him away and kills him. They continue their journey to the Berg's home, discovering along the way another settlement. In it, they find Deedee, a girl who had been hit by one of the contaminated darts two months ago. The survivors from that settlement had abandoned her when she did not sick, feeling that she could only be a demon. The group refuses to leave the girl without any chance at survival and so they take her with them. That night, they hear singing and Alec and Mark go to investigate. They discover some people from Deedee's settlement there worshiping a higher entity, hoping that this will bring an end to the rounds of suffering that they have experienced. Mark and Alec are then captured after revealing that they know Deedee and are almost killed until another group of mad people charge the camp, allowing for their escape. Mark and Alec run back to their camp, only to discover it abandoned. They head to the Berg's landing spot, hoping that they might find some answers there. They find the landing pad underneath what appeared to be natural greenery. They sneak in and discover that the Berg group was a governmental group that had designed a virus meant to wipe out a significant portion of the human population in order to make it so there were enough resources for the world after the solar flares. But the virus had mutated and now is infecting everyone including its creators and shows no signs of stopping. This disease is now being called "The Flare" by the government. Mark and Alec are almost caught and only are able to escape after Mark kills one of the pilots of the Berg they are stealing. Upon finding that he enjoys killing the pilot, Mark reaches the conclusion that he has the Flare. They then fly into Ashville and attempt to rescue the rest of their group (who they had discovered had been traded by the governmental group to the religious zealots in order to get them to hold off on their attack on Asheville). As they arrive, they find Lana, one of their group close to death and so they put her out of her misery. They then rescue Deedee and Trina; Trina's mind is almost completely gone, not remembering even Mark, her closest friend. Realizing that they are all about to die, they land the Berg quickly at the governmental outpost in Asheville and teleport Deedee via Flat Trans to the government's headquarters, saying that she is immune to the virus and that the government should use her to try to find a cure to the Flare. Then Alec plows the Berg into the building, killing Trina, Mark, and himself, but also closing the Flat Trans, giving the world a chance at survival. The final chapter of the book then shows how WICKED found Thomas.

Throughout the novel, Mark experiences flashbacks to how they got to the settlement in North Carolina to begin with. Mark is originally from New York City and was on the subway with Trina when the power goes out and the subway is plunged into complete darkness. As they emerge from underground, they feel intense heat and see many burned and naked bodies on the ground. A solar flare has just hit earth and had burned anything on the surface and left a hazardous level of radiation in the air. They quickly retreat underground but are ambushed by a group of street urchins, who want their food and try to rape Trina. Mark and Trina are rescued, however, by Alec, who had been walking by at the moment. They run to the Lincoln building to try to be high enough above sea level to survive a tsunami about to strike New York. However, they don't get to high ground in time and almost die in the deluge. They then camp out on the nineteenth floor of the building, having joined up with Lana and the rest of the group. Eventually, a large ship sails up what used to be Broadway and its crew the building, holding guns at Mark and his group, telling them all to put their hands in the air. All comply immediately except Alec. The man from the ship responds to this by killing Baxter, a member of their group. They then tell the others to load their ship with food and power generators. They all help but as they finish loading the ship, Alec takes out their hostage-takers and steals the ship for the group; it is implied that this how they all get to the settlement in North Carolina.