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.

The Fever Code: Maze Runner, Book Five; Prequel

Fever Code, the final book in the Maze Runner series, takes place immediately before the first book. We see the story of Thomas as he is taken in by Wicked from a young age. He is isolated and forced to change his name from Steven. He gradually learns of other kids, but still gets special privileges. He, along with a select few others get to help design the mazes. As part of it, he is able to view what happens. He is shocked to see that the monsters inflict real harm and that boys kill each other. That is not the only blood he has on his hands. The new chancellor tasks him and other immune kids with giving lethal injections to Wicked staff members that have contracted the virus. We learn that this new chancellor was treacherous, and had in fact spread the virus, and was later spreading false emails from others to explain it. Thomas thought he was going into the maze with his memories intact, but had them wiped at the last minute. He is regularly double-crossed.
Wicked is portrayed as a stereotypical government agency that exists so that it can exist. It's predecessor had initially launched the virus to help control the human population after sun flares wrecked havoc on the environment. After the virus spun out of control, they were tasked with finding a cure. They would adopt any means to justify the ends, including ripping children from homes and killing their parents. They employed gruesome means of controlling the children in their justification.
This book continues on the theme of "beware unintended consequences". Is it worth it to throw away human civility in the quest for a miracle? It seems easy to justify. If the miracle does materialize, everyone would be saved. If it doesn't, then everyone would be dead. Though the mortgage of morality in quest of the miracle may be the very thing that keeps society from the peace it needs.

The Death Cure (Maze Runner, Book Three)

Each book in the Maze Runner series ends with the kids "escaping" the fake world to get into the real world. Then the next book picks up with a new level of "fakeness". In this third book, we think they are really in the real world. Is this actually the real world? Or is this another level of fakeness? We learn more about the "flare". Most of our characters are immune to it. They are studied to help find a cure. Their immunity lets them do things others can't. However, they are also heavily discriminated against by other people in the world. They hook up with another group that somewhat seems to be their allies, but has different goals. They are in Denver, which seems to be a fairly modern city. There are officers around that try to get rid of all the sick people so as not to contaminate the healthy. The sick are sent to a special "community" where they can live the rest of their life in happiness. However, with people going mad and having little to live for, it had devolved into squalor. These "cranks" decide they will break out and take over the city. Meanwhile, those with immunity had been rounded up and sent into to the "wicked" maze. Our heroes rescue them just in time and then go through a teleportation-like thing to a pastoral field where they can live happily ever after as the saviors of the human race. (However, in the process, many people die.) Our hero, Thomas, shoots and kills one of his friends who has the flare. He later kills a Wicked leader with his bare hands. He is no longer innocent of death. It could be argued that these both were near death anyway, but he still killed them. There is plenty of other violence and narrow escapes from catastrophe. (Things do seem to be just a little too close to be believable.)
Wicked had been tasked with finding a cure for what was apparently a biological weapon. People put their hope in this cure, and assumed that any ends would justify the means. People were lax on containing the outbreak because they though a cure was imminent. Alas, even with great effort, they were not able to find the cure. One leader with foresight had also set out a "plan b" that would put a bunch of immune people in a remote area. They would build up their own society and continue the human race after the rest of the world had fallen apart.
This "plan b" seems to be a wishful-thinking cop out. Could an area really be so remote that nobody else would discover it? Would society really disintegrate so fast that everybody would be cannibalized? There is potential for a couple more series exploring the "immune" society and the "collapse" of primary society. Would some of those immune be able to survive in the primary society? Would the isolated immunes turn on themselves? Could a society whose leaders killed in cold blood really continue peaceably? Is this saying something about some of our current problems, like climate change? IS it best just to find those that can deal with it, and let other parts of the world flood away? And we still have many open questions about why there is such a need to control the minds of people, and why they felt it good not to get memories back. And why was so much violence necessary? Many questions are left unanswered at the "end" of the series. IT seems obvious that additional books are needed.

Scorch Trials: Maze Runner, Book 2

The second Maze Runner book does not feel quite as dark as the first, thought it is very violent. It is also confusing. What is real? What is imagined? Did they escape the "Wicked" world, or are they just participating in yet another trial of that world? Are they really part of something that will help save the world? Or are they part of an cruel scientific experiment? Are the people that die really dying? And how did all these other people get there? There seem to be more questions than answers.
The book starts out where they left off in the first Maze Runner. However, things get weird. The girl disappears and is replaced by a boy. He had lived in an alternate experiment where he was the only boy among girls. He could also telepathically communicate with a girl. However, that girl was shot at the end. They see new things tattooed on their skin. Their lodging seems to do weird things. One day a man appears and gives them their "quest".

They go on the quest. They discover the alternate "girl group". They also run into some other "normal" people. In one case, Thomas is shot by somebody with an old gun. He finds himself whisked out of the world and operated on. Having people die seems fine, but it must be in the way expected.

In the end, Thomas is betrayed only to find that is the way out. We are told this is the end of the trial and now they will be in the real world. But do we believe it? The book goes overboard playing with "reality" that it is difficult to care. Is this the real world? Or is it fantasy? Does it matter? Is the real world one we would care about? That is the important lesson for a reader. The world is very different, yet it is set in the values of today. Would that realistically happen?

Maze Runner

A boy wakes up in a world with no memories in a world he does not understand. He discovers that it is a world with just boys. A new one comes every month. They get electricity and other basics provided for them. However, they have to work to provide food and solve a maze. They hope to sometime escape and get out. However, many of the boys get attacked by monsters and die. Some get stung, but get an anti-venom that causes them to undergo a changing. They get some of their thoughts back.
One day a girl appears, bringing on the beginning of the end. They finally make their way out of the maze, only to find it was part of a horrible experiment. The earth has been smitten by a plague. The maze was set up by a company in hopes of breeding special humans that can help come up with a solution. Other humans help rescue them. (This all seems to coincidentally come at the same time.)
The novel is very dark. These kids are locked in a fake world with real monsters with real death. Is this justified if it can bring about a cure for humanity? Ironically, the kids justify much to save a single boy, but find it abhorrent that they may all be sacrificed to save the human race. Does justification simply depend on free choice?