A group of people have banded together after the ravaging of the sun flares. In this group are the young adults Mark and Trina, childhood neighbors and friends, and now lovers. The group also includes the seasoned ex-soldiers Alec and Lana, and other stray teenagers Darnell, the Toad, and Misty. They are living in a settlement out in the woods with other people. The sun flares devastated the earth almost apocalyptically. Mark has flashbacks of the events of the flares, and these are interspersed throughout the story, usually in the form of dreams.
Mark is returning home from school on the subway along with Trina when the power goes out on the subway. Everyone leaves the train; Mark and Trina get off as well, only to hear screaming and see burning bodies. As they escape through the tunnels, they are first cornered by criminals, and then saved by the ex-soldier Alec. Alec takes them into their group, which includes Lana, Darnell, the Toad, Misty, and Baxter. The group escapes from the tunnels, following a narrow run-in with violently burned people, and a cascade of boiling water from the flooded ocean. They spend weeks in New York’s tall Lincoln Building, surviving off of junk food. They are able to survive the solar radiation this way. One day, a boat comes down the flooded streets of New York. Its violent passengers shoot Baxter for no good reason; they demand food, supplies, and fuel from the group. After loading up the boat, Mark and his friends overpower the pair on the boat, and use it to guide themselves to safety in New Jersey. As the first rain finally begins, Mark and Trina admit that they are romantically interested in each other.
Sometime later now, Mark is hoping for a good day. He wakes up in the morning, banters with Alec, and then goes up to find Trina, who is reading by a stream. That day, however, a government aircraft called a Berg arrives and shoots darts all over the town. People who are hit with them immediately go down, and many start bleeding. Darnell is hit. Mark and Alec, however, manage to climb aboard the Berg, desperate to know why it came and did what it did. The Berg’s pilots commit suicide by crashing it in the woods. Mark and Alec manage to salvage a workpad device from the craft, which reveals the headquarters that the Berg came from. Mark also discovers that the darts contained a virus. They hike back to the village, where they find that almost everyone who was hit by the darts died. However, Darnell did not. Instead, the teenager is going crazy. He complains about a headache, and is bleeding a lot. Mark hears Darnell kill himself violently. Lana concludes that the virus must be mutating, because it affects people in a variety of ways. The group prepares to leave and go to the headquarters where the Berg came from, but Misty feels sick and stays behind. The Toad, her best friend, insists on staying with her. The group recognizes that they must have all caught the highly contagious virus at this point.
A few nights later, the Toad comes back to his friends, but is already showing signs of insanity. Alec kills the Toad quietly in the woods to put him out of his misery. Later, the group stumbles across a village, where the only person left is a little girl, Deedee, who was abandoned by everyone else. The girl was struck by a dart and must be infected, but she is so young that the group takes her with them. Mark and his friends hear chanting and singing as they go on. Mark and Alec go to check out the sounds, leaving Lana, Trina, and Deedee behind for a bit. They discover a crazed cult dancing around a fire. The cult villagers are the ones who left Deedee behind. The crazed people are led by a man named Jedidiah, who claims that Deedee conspired with the demons who led the darts to come upon them. In the midst of this craziness, another group of villagers attacks the ones who are dancing. Mark and Alec escape, but they find that Lana, Trina, and Deedee have been captured. Mark and Alec head for the Berg headquarters site.
Mark and Alec manage to get inside the facilities when a Berg lands. Everything is underground. They hear people talking about how the virus is already nicknamed the ‘Flare’. They come across an old man named Anton, who is terribly upset at what has been happening. Anton’s coworkers are going mad, and they are having a meeting downstairs in the facility. His coworkers captured Lana, Trina, and Deedee, and gave them back to the cult of villagers in order to buy themselves time. The crazed cult of villagers was a test site for the Flare virus. Mark and Alec spy on Anton’s coworkers, led by a crazed man named Bruce. Bruce plans on storming the nearby major city of Asheville. There is a Flat Trans transporter in Asheville that would take them all to the real headquarters in Alaska. Bruce hopes there is a cure in Alaska, as they are obviously all going insane here. Bruce spots Mark and Alec; he and his crazed followers pursue Mark and Alec into the Berg hangar. Mark and Alec manage to fly the Berg out. In the process of killing the Berg’s original pilot, who is trying to kill Mark as well, Mark realizes that he has the Flare. He is slowly going insane.
Mark and Alec fly over to the outskirts of Asheville, witnessing the madness of the Flare take over people everywhere. It is terrifying for them to watch, but Alec sees that Lana, Trina, and Deedee have been taken right into the madness of it all. They land and make their way through the violence and commotion. Mark and Alec carry with them Transvice weapons they took from the Berg, gun-like weapons that can dissolve people into thin air. Using these, they are able to get to Lana, Trina, and Deedee, but not without having to kill Lana and put her out of her misery. Trina seems not to recognize Mark when he gets to her. She is also very sick with the Flare. Mark, Alec, Trina, and Deedee fight their way back out from the crazy suburbs of Asheville and back to the Berg. While his friends rest for the first time in a while, Mark is restless and explores the Berg. He finds workpads, and discovers documents detailing what is known as the ‘Kill Order’. He realizes that the Flare is not natural: it is a manmade government order for population control. The Post-Flares Coalition of joint governments thought that there were too many people on the world and not enough resources. The Flare virus was supposed to kill quietly and quickly; however, it mutated so that it does not kill quickly, instead causing people to slowly go insane. As Mark cries and screams in rage, Alec comes in, rapidly showing symptoms of the Flare as well.
Alec and Mark agree to head in to Asheville to deliver Deedee to the Flat Trans that Bruce talked about. They are not even sure if it exists; however, they have realized that Deedee is immune to the Flare, and that she should survive and go on, even while the rest of them are about to die. Alec shows Mark the controls of the Berg. However, Mark discovers that a few crazed Flare victims have snuck aboard, and so he has to take care of eliminating them first. Mark and his friends see Bruce’s crazy crowd coming into Asheville. They also find a Post-Flares Coalition building just for their personnel. As they land, Mark writes a note for Deedee to carry with her, which announces her immunity to whomever meets her next. Mark and Trina take Deedee into the Post-Flares Coalition building and put her through the Flat Trans. Bruce’s crazies arrive at the door. As planned, Alec crashes the Berg into the building, destroying the Flat Trans. In the last moment, Trina shows that she recognizes Mark by whispering his name into his ear.
Two years later, an immune boy is taken from his infected mother, who cries over his departure. The government officials who take him name him ‘Thomas’. Deedee, now renamed ‘Teresa’ by the officials, meets Thomas for the first time. As the two brightest of the immune children whom WICKED has collected, these two are responsible for becoming the leaders of their group. They will also help WICKED build a Maze. The two become friends, and tell each other their histories.