13 years before the Maze Runner, sun flares ravaged the Earth, killing billions and scorching huge parts of the world.
Mark is hanging out with his friends in a camp when he hears a 'burg', which is a sort of airship. The burg flies over their camp and begins to shoot darts at the group. Darnell goes down, along with many others in the large camp. Mark escapes unscathed.
Mark comes up with a plan with Alec, who is a former soldier, to retaliate against their attackers. They fight their way onto the berg using a grappling hook and shields to protect themselves against the darts. Once inside, they take out all of the attackers except the pilot. Mark investigates the burg, finding the dart ammunition containers. He finds out that the darts are actually filled with a virus called VC321xb47. The pilot only reveals that it's very contagious and that "hell is coming" before crashing the berg.
Mark, a teen, survives the sun flares, staying alive in a group of other survivors, like his best friends Trina, Darnell, 'The Toad', Misty, and their adult group leaders, Alec and Lana. Their group consists of at least 50.
The group is trekking through the forest when they find a girl. The girls has been shot by a dart, but doesn't seem to have the virus. They take her with them.
Mark wakes up the next day. Him and Alec begin the long trek back to their camp. But, when they return, they find dozens of bodies stacked up, and Darnell is found to have the virus. He claims that it feels like something is eating at his brain and he's going insane. The rest of the survivors, which are Mark, Alec, Lana, Trina, Toad, and Misty quarantine Darnell and the dead bodies; protecting themselves form the unknown virus.
The remaining survivors decide to head to the nearest city to find out what is happening, so they leave their camp. It's later that day when Misty announces that her head hurts. Toad decides to stay with Misty 'until the end' because he can't leave his best friend. The rest of the group distance themselves from her for fear of the virus.
The rest of the survivors (Mark, Trina, Alec, and Lana) continue their journey through the forest. The group runs into a sickened Toad later, claiming that his head is going to explode. They figure out that he has the now deadly virus. Then, the Toad attacks Mark, so Alec must put the Toad out of his misery. Alec and Mark leave Trina and Lana to investigate a cult in the forest. The cult attacks the group, and it is then that the two realize that the people in the cult have the virus.
Then, in the midst of the attack, a fire spreads through the forest. The sounds of oncoming crazy people ring in their ears. The crazy people, who have the virus, begin to attack the cult, Alec and Mark. Mark and Alec get away, but when they return to where the left Lana, Trina and the girl (who's name is Deedee), they are nowhere to be found. Mark and Alec follow a trail to a facility on the edge of a cliff. The facility is full of bergs.
Mark and Alec spend a night in the facility before investigating. They overhear a pair of soldiers armed with the dart guns talking about a virus that causes people to go crazy with murderous rage. They say that the virus has spread all over the world and people have started calling it the Flare. Alec attacks one of the guards, and the guard reveals that they were hired by an unknown source to spread the virus. But, the man claims that the virus was just supposed to kill immediately, instead, it mutated and became what is now known as the Flare.
Mark and Alec are eavesdropping on a group of the armed soldiers in the facility. They overhear the leader talking about mutinying the people who hired them to spread the virus in Alaska. It is obvious that these people have the Flare. Shockingly, the leader of the group spots Mark and Alec and the whole group of crazed soldiers bum rushes the duo. Mark and Alec fight their way out of the facility, stealing a berg to escape.
The duo are in the midst of the escape when they find a man infected with the Flare, who Alec calls a 'Crank', and the man attacks Mark. The man reveals that Trina, Deedee, and Lana have been delivered by the infected soldiers to a city up north. The man continues to taunt Mark until something inside Mark snaps, and he pushes the man between the cargo door of the berg. The door closes, snapping the man's bones. Mark finally comes to his senses and he pushes the man out of the door. It is here that Mark realizes that he has the Flare.
After a day of flying (with Alec as pilot), the duo reaches the city where the girls are being held. It is a city run by Cranks. As they search for the girls, Mark spots Lana being attacked by a Crank. The man is brutally beating her. Alec uses a stolen gun to kill the man. Sadly, Lana is already dead. The duo bursts into the house where Trina and Deedee are being held. They fight their way through a bunch of Cranks. The group escapes through the chaos. When they return to the berg, the group realizes that they all have the Flare except Deedee.
Mark is resting in his bunk in the berg when he finds a tablet. He finds that all but one file has been deleted. The file is titled the Kill Order. It is a conversation between the leaders of the acting government of the world, the PFC(Post-Flares Coalition). The leaders talk about how the sun flares have wiped out most of the resources, and that there are not enough resources left for all of the people. They debate on what to do, until one of them suggests a still-in-development virus that "kills quickly and quietly." The virus is supposed to wipe out 50% of the population. Then, there is a later message describing how the virus mutated and wiped out much more than thought possible. The writer says that the remaining governments have formed an organization to find a cure to the virus. The headquarters of the organization, now called WICKED, is located in Alaska.
The next day, Mark suggests that they take Deedee to Alaska, since she is immune to the Flare, and she may be able to help them with the cure. They fly over to Alaska, with Mark, Trina, and Alec getting sicker with every passing minute. Alec is almost a full-blown Crank, and it is only his pure willpower that is keeping the berg flying. The drop Deedee off at the headquarters, and right after, Alec loses it. He crashes the berg, presumably killing Mark, Trina, and himself.
Deedee is later revealed to be the name of Theresa before WICKED renamed her.