The Age of Decadence is a post-apocalyptic game set in the low-magic fantasy period where the imperial experiments in magic had backfired a long time ago. Thus, the future of earth is not at stake, but the cataclysm did turn the once-thriving Empire (based wholesale on Rome) into one struggling to hold itself together and where civil war is slowly brewing, thus justifying the title.
Alien Legacy takes place after Earth has been most likely attacked and humanity there wiped out by the aggressive Centaurians. A number of Sleeper Starships have been launched before that in order to allow humanity to endure elsewhere. You are the captain of one such ship, the UNS Calypso, which has just arrived to its destination, where you find another such scenario. As it turns out, another ship, the UNS Tantalus, was sent after the Calypso to the same system. Since it had a slightly more efficient fusion engine, it ended up beating the Calypso and arriving there 21 years earlier. However, instead of a fledgling colony, all you find are ruins and vague Apocalyptic Logs. Furthermore, since every captain is instructed to assume that his or her ships is all that's left, this trope may very well be true for all the other ships.
Anarchy Reigns takes place after world war has torn the world apart and rampant industrialization by the surviving powers has polluted everything else, leading to rampant illness and mutation.
Most Armored Core games have one or take place after one. Best examples are Last Raven which happens after the unmanned suicide weapons destroy the world in Nexus and V/Verdict Day which take place in the distant future of For Answer after the National Dismantlement War, LYNX War, the conflict with the League and ORCA and it's constant use of Kojima particles.
Barkley, Shut Up and Jam: Gaiden takes place in the Post-Cyberpocalypse, where the world was devastated by a Chaos Dunk performed by Charles Barkley and almost all the great basketball players were massacred in what is known as the Great B-Ball Purge.
Bastion takes place after the Calamity tore Caelondia and the surrounding area (and possibly the entire world) to pieces, leaving only four people and a small army of pissed off Ura ready to take revenge on what's left of the nation as the only known survivors.
The Bayonetta series takes place an eternity after an event called "Armageddon", in which whatever realm existed beforehand was obliterated and split into the 'Trinity of Realities'; Paradiso, the World of Light, Inferno, the World of Darkness, and the Human Realm, the World of Chaos. Apparently this split re-balanced reality to a point where it is now stable, but if the balance between light and darkness skews too much its said a second Armageddon could occur.
Centipede: Infestation, a Centipede re-imagining for the 3DS and Wii, creates a plot for the game. It takes place in an post-apocalyptic world where only a few humans exist and there are many Big Creepy-Crawlies.
300 years after Lavos awakens in 1999 A.D. and lays waste to the world. There's very little food (though the survivors are kept alive via Autodocs), and mutants and killer robots roam the ruined cities and factories. It's your job to Set Right What Once Went Wrong by killing Lavos before this happens.
Happens again in 12,000 BC after the fall of Zeal. When Zeal crashed into the surface, it not only wiped out most of Zeal's own populace but also the vast majority of the "Earthbound Ones" as well. When the dust settles, all that's left of the world is about a dozen or so people and a couple of tiny little islands. Unlike the aforementioned End, there's nothing you can do to prevent this one, since it serves as a demonstration of the disastrous consequences of abusing the powers of anEldritch Abomination.
City of Heroes: Going Rogue: The Devouring Earth has destroyed most of the earth, and mankind is slowly rebuilding. You play as a Praetorian, living under the watchful eye of Emperor Cole, whose island city of Praetoria is one of the few places where mankind can be safe.
Praetoria is in Another Dimension. Primal Earth is still (relatively) intact. This leads to some interesting problems when Emperor Cole finds out there's an inhabitable universe run by a group of people he has deemed unfit to rule themselves...
Combat Of Giants: Mutant Insects takes place in a world 300 years after a meteor crashed the Earth and destroyed human civilization, making way for giant mutated insects to rule the world.
Dangan Ronpa is set in an environment where students are trapped for a long period of time and forced to kill each other. Why don't the police ever show up? An event happened that caused a huge worldwide conflict, and there are no police or even people to control what is happening inside the school.
Dark Earth takes place a few centuries after a meteor strike leaves most of the planet in perpetual darkness from a large dust cloud. Only a few spots are relatively cloudless and allow light to shine through. It is in these spots that the survivors have built cities. Anyone who stayed behind is infected by a "dark sickness" and mutates into a monster.
Takes place 20 years after the Great Collapse triggered by JC Denton, yet in that time, civilization has returned to its pre-collapse level. See Apocalypse Not.
The Game Mod for Deus Ex2027 features this in the epilogue for the Omar ending, after they nuke most of the planet.
Doom, Doom II and Final Doom all take place with practically every other human on whichever chosen planet the game takes place on dead before you even start moving. Although in Doom II you return the favor and totally trash Hell after killing nearly every demon still in it.
Elves in the setting were once immortal and had a magically advanced society before being largely destroyed and enslaved by the humanTevinter Emperium. the third game reveals that the end for the elves came about more due to civil war, with the humans more or less picking over the bones of their civilization.
It happened to the elves again when their new homeland, the Dales, was destroyed by the Chantry. Elven society has since fracture into two remnants: The city elves that are little more than slaves in most cities in Thedas and the nomadic Dalish elves.
Enchanted Arms has this. The fact Yokohama, Kyoto and London are all in the same general 100-km radius area should give you a rough idea of how badly the Golem Wars messed up the planet's surface and layout. Despite the chaotic rearranging of the surface, Mount Fuji somehow got through the mess in one piece.
Etrian Odyssey is established as being one of these in the intro... but the exact nature of the world Before The End is intentionally left vague at first.
Exmortis 2 is all about this: after the war between the human race and the Exmortis, the Earth has been reduced to a barren desert, inhabited only by the few humans still surviving and the Exmortis horde. For added effect, the sky has turned blood red, and the aforementioned survivors are continuously preyed upon by roaming bands of Exmortis travelling upon dark red stormclouds.
The Fall Last Days Of Gaia. Most of the world is reduced to desert, and in many places biosphere is dying off irreversibly. Unlike the majority of spiritual successors to Fallout, it's not the nukes that caused it, though, but the terraformers intended to make Mars habitable crashing over Earth instead as a result of a terrorist attack.
The Fallout series takes place in a world that's been ravaged by global thermo-nuclear war. Most of the world is a desolate wasteland, and of the few places that haven't been destroyed most are either highly toxic, radioactive, or inhabited by the worst scum of humanity.
However unlike a lot of apocalyptic stories which end before civilization starts to get back up on its feet, the world in Fallout slowly gets better with each game and by the time of Fallout: New Vegas (204 years After the End) the West Coast of the United States has been mostly rebuilt and united under a single Nation, and even the rest of the wasteland is occupied by tribes, settlements, and Nation-States.
In Final Fantasy III the whole game starts After the End. The entire world is flooded and in some sort of stasis except for the Floating Continent where the heroes live.
The second half of Final Fantasy VI, which completely alters the world map and jumps forward a year in time... and having one of the most depressing 2D cinematics of all time. And technically, Final Fantasy VI goes through this twice: the War of the Magi, set long before the start of the game, ripped the world apart so badly it took mankind 1,000 years just to rediscover steam power.
There's an argument for the entire Final Fantasy X universe being set "after the end" given Sin's historical decimation of Zanarkand and repeated decimation of any and all towns, plus the belief of the majority of Spirans that the only way to get rid of Sin is to forgo technological advancement.
In Final Fantasy XIII-2, The Bad Future world of 700 AF is this after the second fall of Cocoon. The planet is nothing but a barren wasteland covered in crystal dust and the few remaining humans have slowly died one by one until only Noel remains as the last of humanity. The whole purpose of Serah and Noel's journey through time is to avert this outcome.
In Fire Emblem Awakening, there is a series of DLC chapters called "The Future Past", which take place in a world in which Grima is revived and has all but destroyed the world, leaving Chrom's army to help the few remaining survivors put a stop to all of the carnage. This world is shown to be nearly identical to the main game's future, in which Grima is also revived and from where Lucina and the future children came from; their goal being to prevent that future from happening again.
Fuel takes place after environmental disasters have rendered large parts of Earth inhospitable. In addition to racing, the player character must also avoid various environmental hazards.
By the time Gears of War 3 rolls around, the Locusts have destroyed the last of humanity's refuges (as seen at the end of GOW 2), the COG has been disbanded, the Lambent is running rampant, and the few remaining inhabitants of Sera are fighting for survival.
The 2013 Call of Duty entry, Ghosts, is set ten years after a cataclysmic hostile attack destroys much of US society, turning the country from a powerful global force into a shell of its former self. The government unable to afford a proper military (likely having lost too much money on the recovery effort), the eponymous "Ghosts" are called together from all remaining branches of special forces to form a single spec-ops organization.
This seems to be at least partially why the world in Gingiva is such a Mind Screw: the world has taken over and horribly twisted by some evil megacorporation for materialistic purposes, and almost everyone has been enslaved.
Golden Sun has a variation, where the catalyst event has already happened, but the apocalypse has been happening (very slowly) for hundreds or possibly thousands of years since the initial event. The power of Alchemy was used to create the Great Age of Man, but was later sealed away by the ancients because it was being used for war which threatened to destroy the world. Hundreds or thousands of years later, the world is falling apart at the edges, as Alchemy is what holds the world together. The great civilizations and mighty cities have disappeared completely, leaving behind only legends and a few crumbling ruins, accompanied by Schizo Tech which nobody knows how to create anymore, and can only be operated by those with the power of Psynergy, which has become incredibly rare and Invisible to Normals.
Gyossait takes place after worldwide natural cataclysms caused by the titular goddess of Earth. What's left of humanity lives in small tribes in ruined buildings, trying to survive the progressively harsher climate, mutant attacks, and the defeated goddess's eldritch powers.
The in-game setting for The World R:2 is set after a huge war where humanity kills most of the gods from R:1's backstory.
Also, the entire franchise is based on a computer virus called Pluto's Kiss destroying the Internet years before. The incident is sometimes referred to as the Twilight of the Gods.
Half-Life 2 takes place twenty years after an alien invasion of Earth and revolves about a human resistance fighting the against the occupation. When the G-Man takes Freeman out of stasis and releases him out into the world again, the words he sends him off with are: "So wake up, Mister Freeman. Wake up and... smell the ashes."
One of the more obvious signs that things aren't as they should be is whenever you find a dock - the water line is clearly quite a few meters lower than it should be.
Over the course of the Human-Covenant War, humanity suffers well over 23 billion casualties, a major blow considering that their estimated pre-war population was about 39 billion. Additionally, hundreds of colonies were lost, having been glassed by the Covenant. Nevertheless, humanity has managed to survive the collapse of the Covenant intact enough to begin reterraforming and resettling many of their lost worlds (especially since Covenant glassing was not quite as destructive as initially believed).
Brute history is marked by the First Immolation, a major nuclear war that sent their space age species all the way back to the stone age; when the Covenant first encountered them in 2492, they were just rediscovering radio and rocketry.
In fact, the entire franchise can be considered this to some degree; 100,000 years ago, the Forerunners effectively wiped out all sentient life left in the Milky Way in order to starve out the Flood, with the various specimens they handpicked to resettle the galaxy afterwards all having to start off at a pre-industrial level, regardless of their previous technological capabilities. Even now, none of the surviving species in the Milky Way have managed to fully reattain the technological prowess of the Forerunners.
The Forerunner Saga reveals that humanity suffered this twice in the backstory; once when the Forerunners wiped out their highly advanced interstellar civilization and devolved the survivors, and again when the Halos were fired, which reduced their nascent industrial civilizations back into hunter-gatherer societies.
Would you believe Hatoful Boyfriend has this for its backstory? To wit: Decimated by a superstrain of bird flu, humanity attempted to eradicate the plague-carrying birds with an engineered virus of their own. The birds that survived the latter developed sapience, realized humans were trying to kill them, and fought back, killing even more humans. And now you know why all the love interests are pigeons, and the human heroine lives in a cave in the middle of the wilderness.
Hellgate: London is set in a world where Hell has taken over. Humanity has retreated underground due to the surface being overrun by demons, who have begun to bring "The Burn" upon Earth, an effort to "terraform" Earth to make it like Hell.
One of the worlds visited. Enroth/Colony was a thriving, high-technological and magically developed planet before, within a hundred years, the robots of the most important control center for technology went crazy and overran it, a love drama lead to nukes being used in what was before one of the nicer areas on the planet, a massive rebellion occured against the increasingly tyrannical Governor, and a general alien invasion of the entire civilization led to the entire arm of the Galaxy being cut off from the rest of the worlds, with intrastellar infrastructure and communication being destroyed. The last is specifically cited as having caused 'a fall into barbarism and witchcraft' not only on this world, but on many others...
Heroes of Might and Magic IV starts with Enroth being destroyed by two swords of immense power clashing in battle (we even see a giant mushroom cloud). The survivors flee through mysterious portals leading to a virginal world called Axeoth, as Enroth is literally breaking apart around them. The Barbarians suffer the most, as they naturally fear anything magical, and most refuse to go through the portals. Most of the campaigns deal with the survivors building new kingdoms roughly based on the old ones. For example, the Haven campaign focuses on the new kingdom of Palaendra, populated by the survivors of the Kingdom of Erathia. They are desperately looking for any members of the royal Gryphonheart family to take the throne. That is, Lord Lysander is the one looking, while the people of Palaendra have given up and are perfectly willing to crown Lysander, who keeps refusing (naturally, he turns out to be a lost Gryphonheart heir and is forced to accept the crown).
Most of Homeworld takes place after the Burning of Kharak.
The House of the Dead 4, is set during said collapse; the town you're in is completely abandoned save for a Zombie Apocalypse, and it's implied that the rest of the world has fallen into this condition as well.
Hyper Light Drifter takes place in one of these. While the exact nature of the apocolypse is unclear due to the surreal nature of the cutscenes, the world is littered with dead bodies, broken war machines and ruined buildings. There are also the corpses of massive Kaiju-like monsters throughout the world(who are briefly seen alive during the opening). Most areas outside of the main city are dangerous to travel through due to bandits and murderous creatures, and in some underground areas there are large numbers of corpses, who look like they took shelter and died when the food and water ran out. The world, however, is very pretty, with the end having been long enough ago that many areas are overgrown.
ICEY Takes place in a post apocalyptic future, where the world has been destroyed and nothing remains, except various combat mechs and the apparent bringer of said apocalypse.
Shiver Star, the fifth planet visited Kirby 64: The Crystal Shards, is a snow-covered planet heavily implied to be post-apocalyptic Earth. Outlines of Earth's continents can be seen on its world map model, and its levels include a shopping mall, an abandoned factory, and a fight against a robot in a giant cityscape. According to Word of God, the inhabitants of Shiver Star left long ago for unknown reasons.
In Legacy of Kain: Soul Reaver, Raziel is thrown into the abyss at the height of his empire's power and comes back 1,000 or 10,000 years (or more) later to find it a crumbling, decaying wasteland. Although in this case, there was no cataclysm, just a gradual downward spiral.
The entire concept of the first Legend of Legaia: the bad guys have already won when the game begins, the Mist has enveloped much of the world, the few humans who have managed to escape it live in walled or underground cities, and humanity is on the verge of extinction. Even the ending is bittersweet and symbolizes the End of an Age since Dr. Usha says that all Seru will die off within the next year, effectively throwing Legaia and its Seru-based technology back into the Stone Age.
The entire world had been flooded, and only the Chosen people survived; the rest were killed off. The graphics are so light-hearted that it might never dawn on the player that over 90% of the population of the planet was drowned.
Chronologically long before that, we have Skyward Sword, which has the Lanayru Desert, filled with dilapidated, abandoned factories and burnt out, deactivated robot husks. Activate a timeshift stone, and you'll see them in all their mechanical, electrical, advanced glory. At the end of the game, the Hylians come down to earth from Skyloft and begin a medieval level society that lasts for hundreds, maybe thousands, of years.
Lost Ember has the player exploring the ruins of an Inrahsi city called Machu Kila. It's been so long since anyone's lived there that much of it has been reclaimed by the forest.
Mars: War Logs features an initially successful attempt to colonize Mars torn asunder when the planet's axis tilts, leaving the surface vulnerable to devastating solar radiation. Decades later, surviving colonists eek out an uncertain existence in underground cities, which are fighting each other for water, fuel, and the few remaining relics from the colony's Golden Age.
The krogan homeworld is basically a post-apocalyptic wasteland. First nuking themselves back to the stone age and later being infected with a disease that "controls" krogan birth rate did not really make life on Tunchanka easy.
Given the devastation brought down on civilization by the Reapers once they arrive, it's a safe bet the homeworlds of every space-faring race have become this by the time they're gone, though some were hit harder than others. One point made clear by the expanded ending is that enough is left over for everyone to eventually rebuild.
Technically, the games take place after several ends, since the Reapers have perpetuated their cycle at least several hundred times.
From Jaavik's perspective everything that happens once you bring him out of stasis is this seeing as his entire race and culture was wiped out some 50 thousand years ago by the Reapers.
This is also true of the Rachni, whose species was pretty much wiped out during the Rachni Wars, the Quarians, who lost the war against the Geth for their homeworld and have spent the last few hundred years trying in vain to reclaim it, and the Leviathans, who are responsible for the Reapers, their species reduced to a handful of individuals descended from the generation harvested to create Harbinger.
The Mega Man timeline is complicated. Every series but the original has a point either in-series or in-backstory could be considered "the end" From a Certain Point of View, from Mega Man X and Mega Man Zero'sColony Drops, to the war that took place between them that killed the vast majority of humans and Reploids, to the End of Humanity in Mega Man Legends, a series where the MacGuffin is the last remaining sample of intact human DNA. Mega Man Star Force takes the cake for least ambiguous End in an alternate timeline found in the postgame of the second game, which is the darkest point in the metaseries.
Metal Walker has this, as a huge explosion turned the landscape into an unforgiving desert populated by killer robots.
Metro 2033 (and the book that it was based on) have the remnants of humanity inhabiting the Moscow metro system after a devastating nuclear war. And that's just the situation of the living, as apparently, even the afterlife was blown up.
"It appears that the devastation we brought upon ourselves was complete. Heaven, hell, and purgatory were atomised as well. So when a soul leaves the body, it has nowhere to go, and must remain here, in the metro. A harsh, but... not undeserved atonement for our sins, wouldn't you agree?"
Metroid has an interesting variant in exploring the remains of fallen alien civilisations, often finding an Apocalyptic Log of how they fell. Particularly in the Metroid Prime series.
Mortal Kombat 3 has Shao Kahn destroying much of the Earthrealm, with the main characters being among the survivors of the initial harvest of souls, hunted by extermination squads who are tasked with eliminating threats to Kahn's rule.
The Neverwinter Nights 2 module-building community has given us the White Rose series, set in an ice-age-type post-apocalyptic world.
Nexus Clash is set During The End. What's more, since it's about an Eternal Recurrence, player characters are trapped in a cycle, fighting in one apocalypse after another and unable to experience the worlds whose fates they're fighting over. Characters' attitudes toward this truth range from noble sacrifice to utter horror.
A New Beginning has a brief section that takes place in one of these, after the world has been devastated by climate change. The Time Travelers who arrive there are from further in the Bad Future, where the last remnants of humanity live in sealed bunkers because the surface is completely uninhabitable. The whole point is to try to prevent the bad future from occurring by getting modern civilization to focus on greener sources of power.
Nihilumbra doesn't show you much of the world (since you're too busy trying to dodge The Void), but the City you do get to see is completely empty, implying that the Void has killed everyone else a long time ago. Judging by the City being completely empty, it doesn't seem like this particular world has anyone left alive.
The Panzer Dragoon franchise pulls this off twice, as well. The series starts a thousand years after a great civilization "perished into dust". By the time Saga has rolled around, the last remnants of civilization have been pushed back a bit further thanks to the destruction of the terraforming Towers, an event known as "The Great Fall".
Phantasy Star Zero did it too, set on an Earth that's been thoroughly blasted by a Dark Falz-possessed supercomputer called Mother Trinity. It happened so quickly and thoroughly that the period of destruction is known simply as the Great Blank, because nobody actually knows what happened.
Phoenotopia subverts this; the ancient humans who went to space expected Earth to be stuck as one after the war, but it got better. Played straight in the Dread Lands, which are still as war-torn as ever.
The Pikmin planet, called PNF-404 in the third entry of the series, is confirmed by Word of God to be Earth in 250 million years, long after humanity has gone extinct. The Earth is now inhabited by bizarre creatures barely resembling anything from the real world, and the only remnants of humanity are small fragments of buildings, broken pottery, tiny barriers of different elements, and the various "treasures" the main characters collect.
Piratez, a mod for Openxcom, takes place centuries after a lost game of the vanilla X-Com, when Earth was incorporated into the alien empire and most humans have been turned into mutants. In fact, all of your pirates are mutants too, and terror missions are replaced by pogroms against mutants.
The Visual NovelPlanetarian takes place in a future world that is slowly dying after a devastating war that killed off most of humanity.
PokéPark Wii has what is possibly the most lighthearted take possible on this trope as a background element, at least as far as the park itself goes. It's unclear if humans are still around elsewhere or not.
The Pokémon Mystery Dungeon series. There are broken down human structures and most Pokemon know what a human is, but they regard them as fairy tales and everyone is extremely surprised when they learn the player character is a human. Special mention goes to the Explorers games' Bad Future for being after the end of the after the last end.
In fact, some fans speculate that the main series itself takes place After The End. One theory goes that Pokemon came about due to a machine going haywire which caused a nuclear holocaust. The people that survived either remained unchanged or became the more humanoid Pokemon like Jynx, Mr. Mime and others, while the animals that survived became Pokemon. The whole theory can be read here.
Implied to be the case in Portal 2, although its unclear if the world has actually ended or if the computers running the place merely think it has, on account of the fact that the whole facility has fallen apart in the time since the events of the first game. Although given that it shares a universe with Half-Life, the implication is the Combine invaded while Chell slept.
Then we learn that Aperture apparently saw things coming and managed to take some steps. For the longest time, players thought Chell was the only human in Aperture, but the end of Portal 2's co-op campaign reveals a giant fault full of inhabited cryo-pods: enough "test subjects" to keep GLaDOS busy for a long time.
Then GLaDOS proceeds to burn through all of them in about a week.
Primal Rage shows in its Attract Mode that the world was hit by a giant asteroid, laying waste to all civilization... and awakening a number of powerful, ancient lifeforms. They now face each other in one-on-one deathmatches in order to determine which of them will be the god of "New Urth".
id Software's RAGE takes place a hundred and six years after Earth was decimated by real life asteroid 99942 Apophis. The protagonist, a survivor who was put in a cryogenic time-capsule refered to as an "Ark" due to a massive international project known as "Eden Project", awakens to find Earth taken over by a tyrannic governor and finds disorder and chaos throughout the land.
Rebuild takes place after a Zombie Apocalypse. Unlike most examples of this trope, the whole point is your trying to rebuild society, secure the city and possibly even cure zombieism.
The Reckoning is set in the USA in 2019, a few years after a Zombie Apocalypse. The area is full of abandoned buildings, improvised settlements, wandering infected and raiders. This being a Mount & Blade: Warband mod, the core of the mod is to take part in the war between US Army remnants, Confederacy nostalgists, Neo-Nazis, Rednecks, and Raiders, either by choosing one faction to join or by creating your own independant empire.
Subverted in The Reconstruction. The game doesn't start out like this, but an apocalypse happens towards the end that turns the final chapter into an After the End scenario.
Resonance of Fate takes place long after humans polluted the Earth so badly that they couldn't live on it anymore due to extremely high cancer rates. The last enclave of humanity live in and around a giant air purifier built by their ancestors and have no idea the outside world exists.
7 Days to Die takes place after a Third World War. Oddly enough, Navezgane seems to be perfectly intact, aside from it being surrounded by a nuclear wasteland and the entire population withstanding of zombies.
This may be a stretch, but Shadow of the Colossus may apply, in a sense. Wander travels around the Forbidden Lands, which is devoid of human life, save for Wander himself. However, if one looks carefully (and does a lot of riding), traces of a prior civilization can be found, namely at the altar area in the desert that triggers the 13th colossus, and the "closed off city" that the 14th colossus resides in. Certainly not an end of all humanity or life, but an end to a civilization (maybe?), nonetheless.
The games in the Shin Megami Tensei series all take place after the end of the world, for the most part. The nuclear apocalypse occurs about a fourth of the way through the first game, when God sends Thor to nuke Japan in order to get rid of the demons.
Megami Tensei II starts around 35 years After the End after a nuclear war combined with a demonic invasion sent humanity fleeing to the bomb shelters in 199X.
Although the world of Skies of Arcadia is set during an age of exploration, similar to the era of when Spain had numerous colonies, it is technically set way after the end - that is, after the Rains of Destruction fell and destroyed what the characters refer to in-game as the Old World, which was said a technological utopia until the events leading to the rains. Society has long evolved again since then, and it's found later that the only remains of the Old World that are left, along with the Gigas, is Fina's home, the Great Silver Shrine. Said shrine hosts the very elders that called down the rains in the first place...
Splatoon takes place approximately 12,000 years after humans were driven to extinction by the rising sea level, after which marine invertebrates evolved to live on land and became the Inklings, Octarians, and other creatures seen in the game. The character Judd is possibly the only mammal left on the planet, having been placed in a specially-designed pod that released him after 10,000 years. The developers also go on to state that the game's Splatfest events are the result of the Inklings receiving radio waves from our time that have gone into space and been reflected back to Earth, and interpreting our banal arguments as messages from a divine power to determine to superiority of bread to rice or cats to dogs. This additionally explains why they would have little understanding of what humans were as a species, thinking that our game consoles were altars of worship, but have great knowledge of things like Transformers and Spongebob Squarepants.
The series S.T.A.L.K.E.R. partially subverts and even inverts it. Yes, the place you're living in is a giant completely irradiated version of the western parts of Russia, but everywhere else is not only going on as usual, but completely thriving at the expense of Chernobyl by using the area as scientific research.
Submerged takes place in a half-drowned city after climate change has flooded the world.
Technically, every Mario game after Galaxy would qualify as After the End.
In Super Paper Mario, Count Bleck's goal is to destroy all dimensions (Including Heaven (the "Overthere") and Hell (the "Underwhere")) by sucking them into an interdimensional black hole called The Void, and successfully does so to one. When revisited, the remnants are very different from most examples of this trope: the dimension is completely blank, save for a straight line indicating the ground and the occasional black outline of a pile of rubble; there are no survivors. Dark stuff, for a Mario game.
Tales of Symphonia, takes place some 4000 years after a great war very much like the above one but even more damaging in its effects (at any given time 50% of the world is suffering massive resource depletion), with mankind being prevented from advancing beyond the medieval stage by a powerful theocracy (to keep them from overtaxing the limited remaining resources). The heroes fix that, even restoring the magic tree which provides the resources and destroying the theocracy - setting mankind up for the disastrous great war mentioned in Phantasia.
Heavily implied in The Talos Principle, with the audio and text logs you can read. It's suggested that humanity destroyed itself with its technology, likely through climate change.
This is the case with the UFO Afterblank. The first one, UFO Aftermath, begins about a year after an alien attack that has killed 70-80% of humanity. The sequel, UFO Aftershock, is set after the bad ending of the first game. By the time of UFO Afterlight, things get so bad on Earth that humanity has to leave it outright and you control the colonists on Mars.
And now, a successful Kickstarter campaign by the game's lead designer, Brian Fargo, has brought about Wasteland 2 a sequel in the style of a Tactical RPG, due for release in late August/early September of 2014, and currently available as an early-access title on Steam, though for a higher price than the final game will be on release.
In Wizard 101 the player arrives at the worlds of Dragonspyre and Celestia after they had been destroyed by the Dragon Titan and the Storm Titan respectively. Dragonspyre looks like hell arrived in a large medieval East European city, with rivers of lava and bones littering the ground. Celestia is the equivalent of Atlantis except the Piceans and Crustateans have since found it and are beginning to build their own empire in the ruins.
World of Warcraft's expansion pack Cataclysm, sunders the land of Azeroth, leaving players to experience a world full of floods, volcanoes and earthquakes with many major settlements and areas destroyed.
The Alliance has it rough as the Horde invades Northshire and Elwynn Forest while Orgrimmar is subjected to Fantastic Racism as most of the non-Orc residents are forced to live in slums or leave entirely.
This is actually the second time that Azeroth had an After the End scenario. Ten-thousand years ago, the Well of Eternity imploded, causing the sole continent to split into what there is today. It's noted in one of the Expanded Universe novels that the event happened so quickly that the heroes barely made it to safety. While it wasn't seen, we can pretty easily conclude that hundreds of thousands died - certainly, most of the night elf empire was completely obliterated.
Third time when you include the civilizations ruled by the Old Gods. Azeroth was originally ruled by the Old Gods and populated by their various servant races, such as the elementals, Mantid, and Qiraji. The Titans destroyed this world order, killing or imprisoning the Old Gods and reducing their servant races to shadows of what they were. While the new world is friendlier for mortal races, it was definitely an apocalypse for the world's original inhabitants.
Azeroth actually had it relatively easy. After the Orcs were corrupted by the Burning Legion, Draenor began slowly dying due to demonic corruption and Gul'dan shattering the links between the elements and the Orcs. Ner'zhul created a massive number of portals for the Horde to escape through, with the resulting release of magic tearing the entire world apart. Outland is all that remains of Draenor, a shattered continent floating in the Nether. This has since been Ret Conned by Garrosh traveling back in time and convincing his father not to drink Mannoroth's blood, instead, forming the powerful Iron Horde without dependence on demons.
X-Mercs is a Freemium clone of XCOM: Enemy Unknown, whose setting appears to be a mix of Command & Conquer and Defiance. A meteor shower brings with it a strange organic blue crystal with properties similar to Tiberium and just as nasty side effects. While the crystals are a valuable source of resources, they also emit dangerous radiation that accelerates mutation in plant and animal life. According to the intro, the governments decided that the Godzilla Threshold has been reached and decide to Nuke 'em the sites of the greatest infestation. Naturally, it turns out to only make the situation worse, accelerating the spread of the crystal and further mutating lifeforms. Billions of humans are dead, the rest live in cities protected by special shields that block the radiation, which suffer constant animal attacks. Earth itself looks like an alien planet with Ruins of the Modern Age. There are also implications that this state of affairs was deliberately engineered by aliens (similar to the Scrin seeding Earth with Tiberium in C&C).
In X Rebirth, the jumpgate network has been down for thirty years following the Argons' attempt at creating artificial general intelligence to beat the Terrans in the Second Terraformer War. The Community of Planets and its member governments are long dead and everyone is at each others' throats over resources. Meanwhile the Xenon are experiencing a resurgence. The Darkness affected each system, but by far the worst off was the Terran colony of DeVries, which was dependent on food shipments; mass famine caused cannibalism. They've gotten better, but their technology is failing faster than they can repair it; most of the population lives on the rusting hulks of old Terran space stations.
Xenogears can count, after all, Miang decided to start a nuclear holocaust so grand that thousands of years later, there are only three big cities left on the surface of the world without most modern technology.
Yggdra Union has 2 examples. Lost Aries is a wasteland which is all that remains of a civilization destroyed by the Dragon of Purgatory. Near the end of the game, the setting's equivalent of Atlantis rises from the sea.
In Yu Gi Oh BAM, the isle of Alba Litora was devastated by a great and deadly battle, leaving little but memories of previous duels in its wake.