The Kill Order (Maze Runner, Book 4; Origin)

Kill order follows the apocalyptic disaster blueprint. The story follow the lives of a band of survivors from the "sun-flare" apocalypse as they are now dealing with the new virus outbreak. The "current time" of the novel has them being shot with a virus by a group of commandos out of a flying object. The story of the sun flare is told via dream flashbacks of one of the characters. They were underground when the initial flare hit. Most everyone above ground was fried. Being underground saved them. However, a few hours later the tsunamis hit and flooded everything. They got above ground just in time, and made it to a high rise where they camped out until things improved. They were eventually able to escape after commandeering a boat from a bad guy (who shot one of them in cold blood.) In the present, they were leaving in an Appalachian encampment. A government group had come in to shoot people with viruses to control the population. The virus was supposed to kill people quickly. However, it mutated, leaving people crazy. Our main party set out to find the source of the virus. In the process, they run into a cult of people that believe the sun flares and viruses are part of a punishment from above for their misdeeds.
The fills in background details for the maze runner series. It does leave a lot of holes in the "disaster" scenario. However, there are just enough details to keep it interesting. Most of the characters eventually succumb to the disease. However, they manage to get the immune girl out to the scientists. It also displays some futuristic technology including vaporizing guns and teleportation machines.