The Last Human: To an even greater extent than the original series. Marceline eventually directly tells Finn how the Mushroom War led to the creation of Ooo, as in this continuity she lived through the Mushroom War herself. The bombs blew open the dimensional barriers, bringing back the magic, and that caused the mutation of the remaining life-forms into the bizarre mutants of the show.
My Name Is Molly reinterprets the games' world as being this. There was a fast-spreading plague that endangered the human species. Children who weren't sick with the plague were rounded up, forcibly turned into animals, removed of their memories, and shipped off to far-away villages to live as Funny Animals. The adults and remaining children were bombed.
"Masters of War" starts with World War III breaking out and devastating America and most of the rest of the world. The rest of the story follows the attempts by civilization to survive and rebuild afterwards.
"South Point" is set years after an Alien Invasion resulted in humanity being enslaved and taken off planet, until Earth is left depopulated. The only people known to have escaped this fate are Danny, Dani, and Jazz.
Hunters of Justice: After Braniac's Alien Invasion and the subsequent bottling of Vale, life has not been kind to those that survived. Only Beacon and the surrounding agricultural district are under law and order; the rest of the city has devolved into complete anarchy, with criminals like Adam Taurus running amok. One such criminal, Roman Torchwick, has taken control of what's left of the industrial district and is now holding the city by the balls with it. The dwindling resources have also caused the economy to shift to a bartering system, and things like dust fragments have replaced Lien as currency. Most of all, however, is the complete sense of despair that hangs over the entire population. Within days of the invasion's end, so many people succumbed to depression that all the alcohol stores were depleted, causing the bars to resort to moonshine. The end result is that suicide rates are at an all-time high, and, in Beacon at least, Ozpin has already started and increased the amount of group therapy sessions to keep what little morale is left up. While the narrative doesn't dive into how the other bottled Remantian cities are doing, there are implications that they are hardly any better off.
Light, Darkness and Paradox has the world beyond the first Tartarus, in which angels have committed genocide on the residents of the surface world.
Stellaron Disaster AU: After the Stellaron landed on Teyvat, it spelled the end of the world. The Astral Express lands in the world long after its people and gods are dead save for the monsters and a single survivor.
Thousand Shinji: The final chapters happen during and after the Third Impact: the world gets wrecked, two thirds of humanity, and the survivors have to rebuild their civilization.
In Tales of the Otherverse, the titular parallel world was ravaged by an interdimensional nuclear war. At the start of the story, it is inhabited by some few survivors scavenging among the ruins, and brigands preying on the weaker.
Dragon Ball After The End: The Forum Quest takes place several centuries after the destruction of Earth, focusing on the descendants of the survivors, who have since all become part Saiyan.
On Hrodvitnon's Tumblr, the Post-Abraxas Genocide Route (based on her MonsterVerse fanfiction Abraxas) follows one possible timeline after the AbraxasVerse canon's end-point, where Godzilla has completely dismantled human civilization and reduced the surviving humans to a more primitive level of technology in order to maintain natural balance.
The Abraxas main story itself is arguably a downplayed form of this, as it's set after the catastrophic events of Godzilla: King of the Monsters (2019) although the fallout is no worse than a Class 1. The story mentions Boston, Washington D.C. and Moscow are all still in ruins.
1983: Doomsday Stories: The stories all take place after a nuclear war broke out in The '80s, and what happened after that, from the perspective of the Nations themselves.
At the End of Days: This happens when the life fibers take over the world completely, though it's not so much after any more than it is during, as Ryuuko mentions the time before, while crazy, was normal.
The dimension Carol, Lisa, and Lily visit during one of the mini arc chapters takes place after it was overrun by cyborgs, and at least Royal Woods lays in ruin.
The "Dark World" omake shows what would've happened had Proto-Lucy not been defeated. Everybody being a zombie is the least of the world's problems.
Antipodes: The story is set ten thousand years after the cataclysmic disappearance of Luna and Celestia, the ceasing of the sun and moon's motion in the sky, and a series of desperate resource wars that destroyed most of surviving civilization. Much of the architecture and technology built before the disappearance of the princesses were either lost to the elements, destroyed in warfare, or inactive for extremely long periods of time.
Fallout: Equestria, along with the countless Recursive Fanfics it has inspired, takes place about 200 years after a magical-nuclear war between the zebras and ponies destroyed almost the entire world, and of what it takes to try and bring light back to the wasteland.
The Palaververse: The Motion of the Stars is set after a war between Equestria and Capra devastated the world, blasting the landscape with destructive magic and leaving Equestria a barren wasteland. As Luna and Celestia perished in the war, the sun and moon were left frozen in place as well, further leaving on half of the world in endless darkness and the other burned by unceasing daylight.
Pony POV Series: Equestria's tribal history seen in "Hearth's Warming Eve" (and to an extent, the modern day as a recovered state) is this for the G2 world, whose late 20th century-level civilization collapsed when Discord's brother Destruction basically nuked the planet in order to prevent the creation of G3 and thus a Class X-4 Apocalypse. The "Gaiden: 7 Dreams/Nightmares" collection shows the immediate aftermath of this from the perspective of the main G2 ponies, and it definitely fits the qualifications of the trope.
Ruin Value takes place in the ruins of a city after Discord taught the people of the world how to harness his magic. The story is actually a Stealth Prequel to the entire series, with Celestia, Luna, and Discord being the genetically engineered products of a much more advanced civilization — humanity.
The Writing on the Wall: The twist at the end is that the seventy one-thousand-years old ruin that Daring Do and company are exploring isn't any sort of tomb at all, but a nuclear waste storage facility left behind by humanity. The titular writing isn't a curse, but a warning from the now extinct species that built it about the dangers within.
A Crown of Stars: The history happens five years after Third Impact. In a very Fist of the North Star fashion, the world is in ruins, scavengers inhabit the ruins and wastelands, and warlords fight over the control of what little is left.
Ghosts of Evangelion happens after Third Impact. Instrumentality wrecked the planet and humans are almost completely gone, but after a while people start returning and rebuilding their world.
Higher Learning: In the original timeline, the humanity has been wiped out and Shinji and Asuka has to raise a family on their own on a devastated world. The epilogue happens after Third Impact: the humanity has been wiped out during Instrumentality, but Shinji's choices allow people returning, and the world is slowly recovering.
I don't want to forget happens after Third Impact. Instrumentality wrecked the planet and Shinji and Asuka had to survive on their own for several weeks. After a while people start returning and rebuilding society, but this is not an easy task because the world is facing war, famine and competition for scarce resources. That new scenario allowed Gendo Ikari to gather the remaining of Evangelion Unit 02 and try to rebuild it to be the receptacle of an artificial S2 engine, which would be used to aid in the several tasks needed to ensure humanity's survival. Of course, he has other plans.
Orchestrating the Silence is another post-Third Impact fanfiction where Shinji and Asuka have to look for ways to survive in an empty world.
The Second Try: Chapters 2, 4, 6 and 8 are set here: Shinji and Asuka are the only humans left on the world and they must learn to survive and open up to each other.
Scar Tissue: Most governments have been reinstated, and the half of world population has returned. However the major cities are in ruins, the roads are broken, the other half of people keeps missing and the returned ones are living on refugee camps as cities are being rebuilt, there is a lack of supply water, crops are damaged and there are riots due to the lack of food and water.
Wake features Shinji and Asuka trying to scrape a living in the post-Third Impact world, as learning how to get along each other.
When She Smiles (Fresh C) starts several months after the Third Impact, when civilization human has recovered most of its pre-TI level of development.
You Are (Not) At Fault begins after the Third Impact has ravaged the world. The first chapters focus on the main characters surviving and scavenging for supplies among the empty ruins after going back to the physical world.
Hours 'Verse: The Hours Other Side sub-series is set in the world Nyarlathotep destroyed at the end of Persona 2: Innocent Sin.
Strange New World takes place fifty years after shadows emerged from the underground and destroyed much of the human population, causing most major cities like Tokyo to become deserted. Most of the survivors have formed small settlements out in the countryside. With no functioning government, survivors not only have to contend with roaming hordes of shadows, but also raiders and crime bosses who prey on the settlements.
New World takes place some time after a yet to be specified event has wiped out human civilization. The main story takes place far enough after that that the main characters are not even aware that there ever was a previous civilization, and know nothing about the the end of it. A subplot about a girl who lived in that time period shows us more of what was happening back then.
Sonic X: Dark Chaos is this for most of the Milky Way Galaxy, largely devastated by thirty years of the Metarex War and Shroud infestation. Most of the worlds in the galaxy are either lifeless or actively malevolent too, with Demons and Angels fighting over the scraps that still remain.
Down to Agincourt is After the End in that the Apocalypse is well under way when it starts—but it's also literally after "The End", the episode it's based on!
Age of Strife: The story begins with the destruction of every major city on the planet with fusion warheads, leaving the survivors to fend for themselves on a Death World.
(based on her MonsterVerse fanfiction Abraxas) follows one possible timeline after the AbraxasVerse canon's end-point, where Godzilla has completely dismantled human civilization and reduced the surviving humans to a more primitive level of technology in order to maintain natural balance.