Alternate Equestria:
This is not the Equestria we know. Twilight never left Canterlot, never met the ponies of Ponyville or found the Elements of Harmony. Nightmare found them first, but before that, she killed Celestia and destroyed Canterlot. Her reign of destruction didn't end there. The darkness would not abate until all Equestria lay in ruin. Incidentally, comets are also within her power. In the chaos that ensued, Discord broke free. He saw that his playthings would die if the darkness persisted, but as he couldn't raise the sun or lower the moon, he made his own arrangements. Though the effect is less visible, the ever-present moon has emboldened the monsters the sea ponies keep under lock and key in the deepest abysses. They're free, and though they're never seen, the evidence is strewn across the shores.
Canterlot Before:
Canterlot pre-cataclysm is as it was before the Summer Sun Celebration, with one exception. This year, the celebration would be in Canterlot, hence why Twilight and Celestia were still present and awake when the stars aligned.
Canterlot After:
Canterlot post-cataclysm was a crucible where desperate ponies fought to escape the crumbling buildings, the firestorm, and the hail of comets.
The Castle of the Two Sisters:
The Castle of the Two Sisters is overgrown with moss and ivy, and the stones are so eroded that the moon is clearly visible through the ceiling, the forest through the walls and shattered windows. On the central pedestal, the Elements of Harmony rest.
The Hive:
Chrysalis's hive is a conglomeration of chitin spires that jut like spears out of the misty marshland her changelings call home. Strange flora and fauna inhabits the surrounding area, but the animals are only intelligent enough to know that the changelings are apex predators to be given a wide berth. Some are not so intelligent.
Manehattan:
Manehattan lies on the northeastern edge of Equestrian territory. It's a sprawling metropolis overlooking the ocean, ponykind's last stand against the encroaching darkness. The buildings and their walls are built to withstand the storms that come off the sea as if it were a watery Everfree Forest. The city has a significant gryphon population, and it's been the site of many failed invasions. The ponies there are hardened and cunning, but neither they nor their forefathers have ever known anything like the darkness.
The Crystal Kingdom:
A thousand years ago, the windigos encased the Crystal Kingdom in ice, Sombra's madness having let them in from the Frozen North. He'd fought them, then, but it was no use. The crystal heart was the only thing that could keep them at bay, and as his heart was no longer pure, it would not hear him.
The Surface of the Sun:
The surface of the sun is so intensely hot and bright, the gravity so powerful, that no one without magical protection of reality-warping magnitude can come near. Celestia's body was vaporized the instant it came in contact, but her consciousness persisted. Now the sun is her body, and wherever its light shines, she sees. The plasma surface churns and spits, and while such solar flares might not penetrate Discord's anti-mundane protections, there's no guarantee that they won't harm Twilight.
Hollow Shades:
Hollow Shades has a reputation as a haven for gypsies, vampires, and demon worshipers, which isn't far from the truth. The bat ponies who live there don't usually drink blood, but they are hunters, outcasts from pony society, and the descendants of Luna's night guards. When Luna became Nightmare, many remained steadfast in their loyalty.
The Ruins of Ponyville:
When the armies arrive, Ponyville has already been reduced to a smoking, fractured husk of its former self. Not everypony was able to evacuate in time, so crumpled skeletons litter the ground, and burnt flesh and burnt hair linger in the air. Craters are everywhere.
The Dragon Kingdom:
The Badlands are only the tip of the Dragon Kingdom, which borders the swamp where Chrysalis's changelings built their hive and extends far south of Equestria and far beneath the earth. The Ouroboros resides there, so massive he'd collapse under his own weight if he didn't have the tunnels around him for support. Only his eye is visible, and when its craggy lid is closed, the passage looks like a dead end.
The Ruins of Fillydelphia:
Fillydelphia, like Ponyville and Canterlot, has been reduced to ruins by the time the opposing forces meet to do battle. The only difference is the totality of the destruction. Hardly anything remains of the once-great city, and shipwrecks litter the shore. Even Nightmare is surprised; it wasn't her doing. Neither was it Discord's. It was the tide's.
Twilight Sparkle:
Twilight is arguably the main character. She's there in the beginning, and she's there in the end. The same can't be said for anypony else. Though she fights like hell to survive and often has to wonder what the point is when things are so utterly bleak, she struggles not to lose herself. How easy it would be to give in. Her purpose in the story, more than anything, is to provide the eyes through which the reader sees the end.
Queen Chrysalis:
Chrysalis wasn't always queen of the changelings. She used to be an infiltrator, and a talented one at that. She learned much about the world on her assignments, and when she returned, she saw how the old queen had become corrupt and complacent. She usurped her and ushered in a new age for the changelings. No longer would they cower from ponies, barely scraping up what they needed to survive. They would take it, by force if necessary. That was her plan, a full-scale invasion, but then the Nightmare returned, and she knew she had to rethink her strategy, or there would be no hope for anyone, pony or changeling.
Nightmare Moon:
Nightmare Moon is the name given to Luna in the false history made up when Celestia, who had grown too fond of her subjects, chose to break the cycle of dark ages and golden ages. Celestia had never opposed her before―that wasn't her way―so Luna was taken by surprise. For the thousand years Luna spent on the dark side of the moon, staring into the abyss between the stars, the Ouroboros whispered to her, driving her mad.
King Sombra:
Sombra was a wise, benevolent ruler once. He was also Luna's consort. When she was banished, he turned to the dark arts in his grief. Shades consumed his soul in exchange for immortality, but for all his new-found power, he couldn't stop the windigos from taking his kingdom, for he had lost his connection to the crystal heart. It's doubtful that anything different would have happened had he learned of his lover's true nature, and what she was destined to do. The Ouroboros cares little for Sombra's contribution, yet he's more a pawn than anypony. Perhaps even a victim.
Princess Cadence:
Cadence is a minor character. More than anypony, she knows that love is the only thing that can carry her fellow ponies through the darkness. She also knows that her cutie mark depicts the crystal heart. With Shining along for physical protection as well as emotional support, she goes to find it and bring it back. She and Shining are also present to provide emotional torque for Twilight at several points in the story.
Shining Armor:
Shining is another minor character, Twilight's brother and last living relative. His presence is a comfort; his death will be ruinous. Notably, he loves Cadence. The feeling is mutual, of course, but it's not out in the open yet.
Discord:
Discord is an enigma. How he came to be is uncertain, but his history is rich and colorful. His actions certainly support his claims to the title of chaos incarnate, but he has been known to show compassion, often on a whim, usually when the end results amuse him. He stole the Elements of Harmony from the Tree of Harmony as a joke, and as an afterthought, before he got bored, imbued them with his soul, that he may never die so long as they existed. Doing so weakened him such that the princesses were able to use them against him, but they still couldn't kill him. When Nightmare shattered them, he was mortal again, but his stored power reverted back to him.
Princess Celestia:
Celestia knows what's coming, and she knows she's powerless to stop it. She and Luna are both mere reflections of the Ouroboros. She knows she's angered him―she's seen it in her nightmares―but until recently, she knew not how he would punish her. She'd hoped it would be just her, but it seems she wasn't so lucky. When she becomes one with the sun, her personality becomes so diffuse that she no longer recognizes herself as having any stake in the world. She's omniscient, omnipotent, and utterly indifferent.
Spike:
Spike was never meant to be hatched, merely to be kept safe, where the assassins that would seek to slay the last of the royal brood couldn't get to him. Ever since Twilight did hatch him, the two have been inseparable. He's a dragon among ponies, and she's a stranger among familiar faces. Apart from Celestia, she's the only family he has. Had he learned of his nature before being forced to join the migration, he still wouldn't have wanted to go. Since he was forced, he has less will to fight the Ouroboros's designs. The tributes that help him grow into the king his people need also help him forget the life he's lost.
The Ouroboros:
The Ouroboros is patient. The offense for which he seeks to punish ponykind occurred a thousand years ago, when Celestia's ponies urged her to defy the oncoming darkness. It knows neither malaise nor mercy. It seeks merely to perpetuate the cycles that define the course of nature and history. Self-preservation, in a way. It never interferes directly, for to release its grip around the planet would be to allow it to break apart, but as the incarnate god of the dragons―who are themselves cyclic creatures―it doesn't need to. Its body wraps around the world several times, and it communicates through telepathy.
Chapter I:
Nightmare returns to the world unopposed, and in the spirit of irony, banishes Celestia to the sun. Then she turns on Twilight.
***
Discord awakens from his eternal slumber, breaks free from his marble prison, and wanders, bemused, among the burning streets and burning ponies of Canterlot. The perpetrator is gone, but an eerie light pierces the sky over the Castle of the Two Sisters in the Everfree Forest.
***
Chrysalis, sensing the wrongness, emerges from her hive to investigate. The unnatural night and the return of the snow―which she hadn't seen since the time of the windigos―so horrifies her that she rallies her swarm ahead of schedule.
Chapter II:
Twilight flees the ruins of Canterlot with Spike on her back. She learns from the other refugees that the ponies of Manehattan are establishing a bulwark, a last bastion of sanity in a world that's been turned on its head in a single, endless night. Despite it being the height of summer, snow comes to Equestria.
***
Cadence has enlisted Shining as her escort to the Crystal Kingdom. The support of the crystal ponies and the crystal heart is their only chance. It's a sort of fail safe.
***
Discord meets Nightmare in the ruins of the Castle of the Two Sisters, sees the fragments of the Elements of Harmony, his soul jars, and offers her an alliance. She refuses, for she has no intention of keeping her victims alive to torment.
Chapter III:
Sombra asserts his dominance over the crystal ponies, having taken the crystal heart unopposed and consumed it. He corrupts their bodies into dark crystal and binds their souls to his will. Flesh ponies will serve him willingly, for their misery will make them prime acolytes in the dark arts, which will further twist their hearts as they did his.
***
Twilight sends Spike away to join the dragon migration, to flee the doomed nation of Equestria, and perchance, to get help. He doesn't want to go.
***
Celestia feels her mind, her entire consciousness, dissolve into the sun. While its sheer magnitude and reach eradicates her individuality, it allows her to see across time and space and into the hearts of every living thing, pony or otherwise.
Chapter IV:
Discord offers to protect the ponies of Manehattan, but his assistance comes at a terrible price. Twilight usurps the obstinate mayor and steps forth to negotiate the alliance. Discord can't move the sun or moon while Nightmare lives, but he's already begun to twist the environment to his liking. He twists the ponies accordingly, that they might continue to live and amuse him. Survival.
***
Cadence and Shining, battered and traumatized, arrive in Manehattan, where they meet Twilight. Twilight tells them what she saw in Canterlot. They tell her what they saw in the Crystal Kingdom. Hitherto, Sombra was another figure of legend.
***
Nightmare sways the bat ponies of Hollow Shades to join her; those who've remained loyal to her, who've kept the traditions alive these past thousand years, she sees fit to spare. But there are those who defy her, some of whom escape.
Chapter V:
Chrysalis appears before Twilight and seduces her with promises of military strength, magical knowledge, and above all, undying loyalty in the darkest chapter of her life. Her disguised changelings are making similar offers to the other ponies of Manehattan, and most have already accepted. These ponies will have the strength to fight, but there are those who never made it to Manehattan.
***
Discord meets Nightmare in the ruins of Ponyville. His victory seems decisive until Sombra comes to the latter's aid. Discord realizes that something foul is afoot and leaves his lieutenants, Cadence and Shining, to aid in his army's retreat.
***
Spike is greeted by the dragons with distrust and taken to see the Ouroboros, who foretold his coming and has plans for him. The Ouroboros tells him the ponies are to blame for the snow. Spike fights its attempts to turn him against his old friends, but when he sees the tributes, fit for a king, his nature wins out.
Chapter VI:
Twilight has been doing a basic "cloak and dagger" exercise with Chrysalis, wherein she tries to wrap a dagger in a cloak of invisibility. When Discord arrives and brushes off how he left Cadence and Shining behind, she unveils the dagger and lunges. Discord doesn't have time for it. He snaps his fingers, turning the dagger into a firecracker, and takes her to see if she can't talk some sense into Celestia.
***
Chrysalis ventures to the sea that she might plead for the aid of the ponies she knows dwell there, but realization soon dawns: the deep horrors they kept have gotten loose. The wind threatens to break her wings, so she flees as fast as her legs can carry her.
***
Nightmare and Sombra are reunited, and from their terrible union, the shades of the fallen, including Cadence and Shining, are raised. Together, they resolve to push Discord out of the world, for he poses the only real obstacle between them and glorious oblivion.
Chapter VII:
On the surface of the sun, Twilight attempts to commune with Celestia while Discord keeps the extreme conditions from annihilating her. Celestia will not hear their pleas, but she does reveal the circumstances that spawned their situation. Determined not to leave empty-handed, Discord condenses a solar flare into a ball of plasma. Half his reason for coming had been to gloat, and Celestia's indifference had deprived him of that.
***
When Twilight returns, Chrysalis informs her of the developments her scouts have reported. Another battle awaits. This may well be their last moment. Twilight decides they should make the most of it. Afterward, Chrysalis forms a telepathic link to impart unto her all her knowledge of illusion magic. It's not a process she takes lightly.
***
Gryphon zealots, the victors of a recent schism, lay siege to Manehattan, believing, in accordance with their version of the legend, that the ponies are responsible for the darkness. Twilight steps out to greet them, and their great war machines.
Chapter VIII:
Cadence and Shining march toward Manehattan alongside Sombra and Nightmare. Unbeknownst to their masters, and each other, they've retained their self-awareness.
***
The opposing forces meet in Fillydelphia and the surrounding plains. The city has been reduced to rubble by the relentless tides. Midway through Sombra's speech, Discord lobs his condensed solar flare into the enemy forces. In that pivotal moment, Shining assassinates Nightmare, who is, after all, a physical god. Seeing this, Sombra seeds his body with a dark crystal and morphs him into a colossus. The battle begins.
Changeling infiltrators, dark magicians, crystal ponies, embittered survivors on both sides, and the shades of their brothers, who fell in the last battle, war for nothing less than the total annihilation of their opposition. Chrysalis commands her foot soldiers through telepathy and keeps a third eye on Twilight, who takes on the colossus that was Shining. Cadence breaks free from Sombra's iron will long enough to help, and to say goodbye to Shining, but not long enough not to turn on Twilight.
Twilight stands ragged over Cadence's broken body, hot, sticky blood in her fur. She's in a daze, but the voice of Nightmare snaps her out of it. The battle wears on.
Gryphon gunships align on the edge of the battlefield. Twilight sees them preparing to shell her position, to end the Nightmare and her with it. Twilight teleports aboard. Nightmare doesn't turn around until it's too late, but the blast doesn't kill her. She rises to assault the gryphon fleet. The captain argues with Twilight, and Twilight can't believe the things she says; she's become a warrior, and the captain notices.
They don't have time to rest on their laurels, as the Nightmare descends upon them. At length, in a ship-hopping battle, Twilight finishes her with the gryphons' machinery, because magic will always pale before the dauntless advance of steam and steel.
On the ground, many lie wounded; many more lie dead. Chrysalis and Discord try to finish Sombra in their way, but their battle goes nowhere. Discord's slapstick style of self-defense can’t harm Sombra’s incorporeal form, but Sombra can’t throw anything back that can’t be turned into a harmless banana cream pie, explosion of flower petals, or some such thing before impact. The stalemate doesn’t last long, though, for Spike and his dragons descend over the horizon, silhouetted against the full moon. One by one, they open their maws, which roil with flames.
Seeing this, Chrysalis teleports herself and Twilight to safety.
***
Twilight and Chrysalis appear in a mountain cave, where they see the forms of the fallen and the broken bodies of the still-living engulfed in a wave of dragon fire that leaves nothing but bone and ash in its wake. Chrysalis sees her children reduced to smoking husks, hears their pleas for salvation, and feels all the love they earned flowing back to her. The excess magic threatens to destroy her, but she channels it into Twilight, whom she knows can take it, forcing the wings of a princess to sprout from her back. Chrysalis vows not to lose her too. Without Nightmare forcing the sun out of the sky, she hopes they’ll be able to return some semblance of order.
With her new power, Twilight tries to lower the moon. She fails.
Chrysalis uses her remaining magic to start the sun creeping into the sky, leaving her weakened but conscious.
Most of the dragons take to circling overhead, their thunderous wing beats fanning the flames. Their leader descends on Sombra, who stands, defiantly, after all others have fallen. He bargains with the dragon, but it doesn't hear him. The world is not his to destroy, only the pony world, and in that, he's succeeded. It uses its magical green fire to banish him to the oblivion he so desires, from which he may never escape.
Chrysalis sees this and explains that as long as Twilight, the last pony, harbors hatred in her heart, Sombra will forever be imprisoned in the space between spaces.
Twilight doesn’t feel hate. She doesn't feel anything at all.
Chrysalis holds her and assures her that it will pass, but even the capacity for hate is enough to sustain him. She could purge it, but not without removing all Twilight’s emotions. Otherwise, if Twilight really is the last pony, Sombra’s existence will only end when Twilight’s does, which will only be when Twilight chooses.
Chrysalis has nothing and no one else left to live for, so Twilight doesn’t have to worry about leaving her behind; she’ll gladly descend into Hades by Twilight’s side.
Twilight asks if Chrysalis believes in Hades.
Chrysalis isn’t sure. If she was, she wouldn’t have to think twice about leaving the world behind to be with their loved ones.
Twilight wonders if Cadence chose to die.
She probably accepted the possibility, Chrysalis explains, for even princesses can be killed before their chosen time, and the Ouroboros has evidently decided that they’ve overstayed their welcome―otherwise, Celestia and Luna would both be revived when the ages shifted and they were needed again. That doesn’t matter, though, because the Ouroboros never interferes with the world directly, and Chrysalis will protect her from any danger he sends their way.
For the first time in months―perhaps weeks, though it feels like years―the light of Celestia, the sun, shines over the ruins of Equestria.
The dragon, satisfied that Sombra and his armies are no more, turns to look directly at Twilight and Chrysalis, launches into the air, and alights on the mouth of the cave.
Though she’s still weak, Chrysalis pulls herself to her hooves and prepares to make good on her promise.
The dragon has grown immensely from the tributes of its subjects, but even as the new dragon king, it's still recognizable. It's Spike, the last of the royal brood. Dragons and changelings are old allies―one of their ancient kings taught the changelings teleportation magic―and though the Ouroboros would have Spike make an example of all ponykind, Twilight included, the king is his own dragon. He's kept his name.
Spike was the last remnant of the royal brood, stolen as an egg both to protect him from would-be assassins―because immortals look out for their own―and to destabilize the dragon kingdom. His return ushered in a new age for the dragons, as it will for what remains of pony kind. There are remaining ponies―bat ponies, mostly―but they’re few and scattered far. The fate of the sea ponies remains unclear, but it doesn't look good.
Spike allows Twilight and Chrysalis to live, even granting them asylum in his kingdom until they decide where they’ll go, provided they understand one thing: the age of ponies has ended, and the age of dragons has begun. He takes flight, and his dragons follow. They would do battle with the windigos, and they would win. Equestria would thaw, and scaly feet would leave their marks in the muddy earth.
Chrysalis tries to console Twilight by reasoning that Spike’s pony upbringing will make him a compassionate ruler, as much so as a descendant of the Ouroboros can be.
That's not what worries her. With absence from time comes knowledge of time, and in her mind's eye, she glimpses the terrible form of a centaur-like creature with an ape's upper body rearing against the chains that bind it to the deepest pit of Tartarus. No amount of magic will be enough to defeat him.
The dragons would care little for such considerations. As the sun reaches its apex and freezes the sky in an eternal eclipse, the dragons soar over the charred landscape toward the Crystal Mountains in the Frozen North.
