Towards The End Sky

The apocalypse genre is greatly influenced by the post-war (WWII) mentality.  In post-war Japan, which rebuilt after seeing most of their major cities firebombed and their industry destroyed, the concept of an apocalypse was much closer to reality, not the least because of the nuclear bombings.  Similarly, much of Europe's urban landscape was a ruin due to the bombings from both sides, and rebuilding afterward was a colossal undertaking that made it easy for the Soviet Union to take over a massive portion of the continent like it did, through means both forceful and more subtle.  

As a result, most apocalypse genre works in all mediums are descended from the ones inspired by this era and the threat of nuclear war that persisted through much of the twentieth century afterward.  For a generation that had witnessed the disintegration of two major cities and now had multiple hostile powers possessing similar - even more powerful - weapons, it was much, much easier to imagine the annihilation of humanity than it was for previous generations.

Most current works are evolutions on the same ideas as those from that era.  There is a sense of cynicism about human nature, a sense of helplessness when it comes to an individual's ability to effect outcomes, and a sense of desperation for survival that influences preppers and all other sorts of people even today.

I personally would like to offer the most unique variation on the post-apocalypse experience I've seen in a VN (or rather the most modern one).  Komorebi no Nostalgica.

This VN is unique in that, at first, it is difficult to tell that this is a post-apocalypse landscape.  The characters are living normal, peaceful lives in a seemingly super high-tech world, but when they discover an ancient android, the predecessor to the sentient AI androids called the Metosera that now live as independent sapients amongst them, the perspective changes drastically.  While the basic atmosphere remains soft and disconnected from what came before, the characters are slowly confronted with a line of thought that predates their current society and the remnants of the old war.

Spoiler

The android they discover, Cinema, was an android that worked at a video rental shop run by a mysterious 'manager' (who goes unnamed through much of the VN).  Unlike the Metosera, who are often very Vulcan in their logical statements, even as they show emotion, Cinema - despite being technically two generations behind the androids that first allowed the Metosera to emerge - shows a wide range of childish emotions and a surprising degree of innocent insight that startles both the characters and the reader.

However, as Cinema's functions gradually unlock, it becomes apparent that the intent behind her design is similarly alien to the development of the Metosera, who spontaneously developed emotional emulation through pure programming evolution.  Instead, Cinema's every bodily function, every aspect of her design, is put together to encourage the natural development of machine consciousness with only the most basic of evolutionary programming to aid it along.  It even has a built-in flaw she has to overcome in order to become truly sapient.

Moreover, while maintaining her purpose is the service and protection of humans, Cinema feels genuine in a way many Metosera (with the notable exception of Fluorite, the heroine) fail to do due to their isolationist tendencies.  

Also, as one explores Cinema's story, one also runs across the reality of a post-apocalypse world.  Humanity has lost most of its history, due to the universal digitization of the history books and cinema (incidentally why Cinema herself is so valuable, as she has a massive amount of movie data in her data banks), a single terrorist attack essentially obliterated the records of humanity's history during the war between humanity and the AIs (by the way, humanity lost).  Global warming also sank an enormous proportion of civilization under water, and the protagonist and two of the heroines actually explore the underwater remnants of Tokyo in search of a database during the common route.  These ruins remain mostly untouched, despite being underwater, a massive skyscraper mall able to be explored on foot without a suit due to the advanced materials of its construction.  In exploring the underwater ruins and this building, one is confronted with the sense of sorrow and loss, as old advertisements and remnants of people's lifestyle and shopping remain scattered around its floors, as if it was only abandoned a few days ago, rather than a generation or more in the past.

The final, grand route of the game shows Cinema reaching full sentience and sapience, despite the fact that her hardware shouldn't be able to support the AI architecture that conventional theory says is necessary for the purpose.  This triumph of a long-dead man's dream of creating a neighborly, familial AI sapience instead of the former slaves turned equals that are the Metosera is incredibly impactful, especially if you have gone through Fluorite's path, where she undergoes a grand evolution of emotion and gains ground on even much older members of her race.

As one of the kinder, gentler post-apocalypse societies, one in decline despite its technical superiority, Komorebi no Nostalgica is an excellent choice of a representative of the apocalypse genre.

Another example of an interesting apocalypse story would be Evolimit, one of my all-time favorite VNs and written by the same author as Tokyo Babel.  I'm going to spoiler this one as well, since I intend to just talk openly about various aspects of the setting and story.

Spoiler

First, the protagonist Shiranui and his comrade Shizuku wake up without memories a hundred years after they went into cold sleep, where they are introduced to a society drastically different from the one they are familiar with.  Their memories return shortly, when they confront the reality they are on Mars, not Earth, but this only makes sense, since they were originally part of the first wave of colonization of the planet.  

Evolimit's world is one where society has taken a drastically different turn due to two major factors, the existence of the personal evolutionary substance known as 'Patch' and the threat of the Barbaroi, massive AI mecha that constantly threaten to slaughter the denizens of Mars few cities.  At some point after Shiranui and Shizuku's memories cut off, their expedition was wiped out, and most tech was also wiped out for the second wave of colonists due to a viral infection that turned all machines against humanity.  Without the discovery of the Patch, humanity would have gone extinct on Mars shortly after their arrival.  

As it is, they are living in a modern-seeming, post-tech society that was created through desperate efforts of the early settlers of the second wave of colonists and the sheer power of the 'Star Priests/Priestesses' who serve as mayors for the city-states, creating the environment-maintenance Patches and serving as judge, jury, and executioner in addition to their role as administrator.  Despite this, it is not a dystopian society, but rather a somewhat feudal one posing as a modern society.  Like an isekai medieval world, it is not uncommon for villages to get wiped out by Barbaroi (monsters), people just accept they can't travel without combat power, and people sort of naturally fall into their roles when it is necessary, like a pure military society.

The equalizing power of the Patch, which vastly improves the body while providing a single unique ability to every individual, has removed social inequality while also maintaining a situation where everyone is on war footing for several generations.

The sheer tragedy of this world becomes evident when the Disasters, the threat from Shiranui and Shizuku's past reemerge and their memories of the individuals behind the Disaster come forth.  Their dearest friends, warped horrifically by the power of their Patches' evolution into facsimiles of the great people they were, are the true enemies of the denizens of Mars, living tribulations who want nothing more than for humanity to overcome them... but won't stop until they have been defeated, a feat that is virtually impossible for the average Patch user.  

The false logic implanted in them warps their consciousness (with the notable exception of Phantom Killer, who is a true nihilist) and causes their love of humanity to make them want to force tribulations upon them.  This is done by acting on their deep and visceral understanding of humanity's flaws, brought on at least in part by their exceptionality as human beings before they were changed.  Each of the Disasters was a genius, an exceptional individual who was selected in a one in one hundred thousand selection process for the first wave, as well as being one of the leaders of those people who stood at the head of humanity.  

Their immense potential as Disasters is all the more terrible for how great they were as people.

Baldr Sky (all of the series) is a perfect example of the post-apocalypse and apocalypse genres.

Spoiler

  It is based decades after a world-devastating war that changed the shape of continents and erased most of the human population.  Most of those that have survived are living perpetually in the virtual realm while consuming nano-reconscructed soylent green instead of real food.  Society has mostly broken down, with only a few places creating an illusion of relative peace.

In Skydive, the threat and benefits of AI, as well as nanotechnology are brought to the fore, even as the protagonist desperately seeks revenge and redemption.  Having witnessed his girlfriend dissolve in gray goop, he is obsessed with both preventing the disaster of self-replicating nanotech from repeating itself and getting revenge on those who caused the disaster.  While the focus is on his personal story, there is plenty of information about the world around him, which is pretty hopeless, overall.

In Baldr Sky Zero, we are given another scenario (based in the ruins of South Asia rather than Japan) where a group of mercenaries fights their way through a virtual and physical landscape that is the result of the creation of a true war economy.  Human beings are created, experimented on, used up, then recycled back into the system.  The virtual world is simply a realm where the lambs are led to sacrifice, while the physical realm is where they can briefly play before their young lives are cut short.

The wars themselves are without meaning beyond the development of useful virtual and physical technologies, their theft, or their destruction.  Corporations rise and vanish with alarming frequency, and children sometimes have to auction their own body parts off for money before they are killed in snuff videos.  As a world, it is perhaps the most horrifically dystopian post-apocalypse setting I've seen.  Muv-Luv Alternative at least had humanity united against an outside threat, whereas in this setting, humanity was just doing all these awful things to themselves.