The rainbow magic of the Elements of Harmony engulfed Twilight and Celestia, much to Shining Armor's horror, but he couldn't do anything anymore. There was nothing left to do now but let it run its course. However, when the elements struck a perceived threat, they would usually take but mere seconds to fully affect them. Here, however, they had been lingering for quite a bit longer than that, making the bearers realize that something was wrong, and they were direct witnesses to the cause of that realization.
Twilight's medallion shook aggressively while engulfed in the magic, and multiple rectangles emerged from it, floating in the air. They eventually 'joined' each other into a wall on the side and somehow 'grabbed' the magic, crushing it. Doing something that wasn't really possible caused the spell to crash and collapse in on itself and send everypony but Twilight flying away in a surge of magic and power. The rectangles suffused the spell cast upon both Twilight and Celestia and corrupted it before throwing it at Twilight and fusing her with it.
Shining felt his heart sink and despair engulf him as the world around him seemed to vanish when Twilight started screaming from the infusion and multiple large pulses of unknown magic flew out of Celestia's body, crashing into several of the refugees of the outside world, immediately killing them and stripping them of their souls as their bodies immediately began to decay. The stronger ponies screamed in terror, not knowing what to do.
"What in Hades is that thing?" Shining whispered to himself. "It hurts to look at..." He put a hoof to his forehead and struggled to stand up as he was buffeted by the magic surges.
The stallion wanted to tell it to leave his sister alone, to disappear, but as Twilight began to transform, despair engulfed him, and the next surge did to him as it did to his fellow ponies. Now as naught but an extremely powerful skeleton, the new undead waited patiently for its master's bidding as its bones were wrapped in Twilight's magic as Spike's was. It was all that was left of Shining's love for his sister, and he hoped, in his final moments, that he could bring her comfort in the dark days ahead.
Moon Dancer awoke from her stupor and saw bits of something falling from her head. The other mares woke up in the same way and heard cracking and 'tinking' noises. The Elements of Harmony were cracked and falling apart in tiny bits, much to their shock and horror. Seeing what was happening to the survivors, the mares gathered everypony up as best they could and used the last of the magic left in the elements to teleport them away. From what pale yellow unicorn could tell, the surges were only reaching as far as the walls of the castle. She hated herself for not being able to save the ponies in Canterlot City, as did the five other mares, but there was nothing they could do. There was nothing they even understood of the situation.
Equestria soon became engulfed by the Green Sun and the walls between the living and the dead were irreversibly damaged. The weaker of the ponies or just the unfortunates being in the wrong place at the wrong time found themselves engulfed in necromantic energies and turned into undead. Worse still, they all turned into various types that were influenced by their environment. A notorious kind turned into dried, desiccated husks that wandered near salt mines where they were transformed, absorbing moisture around them and almost or outright killing anything that approached their 'territory'.
Equestria, as its inhabitants knew it, was no more. Little pockets existed here and there, fighting against the encroaching dead and eldritch entities that would peer through the cracks in reality and do whatever they felt like. At first, every country in the known world had sealed Equestria into its own lands, but Twilight and Princess Celestia's powers only grew as time went on, corrupting and destroying everything they could find. Eventually, the build-up of magic tore away at the seals to infect and expand beyond Equestrian borders.
Many communities fled underground, hoping to establish a new life for themselves and their loved ones, but those born in the light needed to see the sun every once in a while, and those who gave in to that hunger would eventually see themselves transfixed and warped by the necromantic aura exuded by the corrupted sun, seeing their bodies stretched, expanded, and burnt, turning into a tangled mess of flesh and meat ropes. It left many ponies mentally scarred and traumatized when bearing witness to such a thing.
As the corruption spread, it affected other lands, raising long-dead monsters from the lands and the sea and bringing back the long-dead victims of war and disease. Many undead dragons flew through the skies, trapped in their wars of the past and repeating their lives at those moments when anything broke their routine. The necromancers of Saddle Arabia could barely do anything to save the capital city. Too engrossed were they in their wants and needs that they hadn't trained themselves nor expanded their knowledge on the dead. However, they were still capable of subduing some of the dead, and by their very nature were immune to the waves of magic Celestia unleashed into the world. Luna kept hidden from everything, staying in the cave and eventually vanishing from everyone's minds as they were more preoccupied with this new life of theirs.
The Elements of Harmony, having their own family to care for, ended up breaking apart with their own, individual elements in tow but would eventually return to the Crystal Castle kept safe by the Map of Harmony.
The wildlife wasn't spared from the actions of Twilight. Many beasts ended up as warped as the ponies were and several of the larger monsters were possessed by the stronger spirits and eldritch entities, turning them into misshapen, slavering abominations that prowled the lands to crush and slaughter whatever their many limbs and detecting organs found. Fluttershy was especially affected by such occurrences, but Angel Bunny was far too angry and stubborn to be possessed. His sturdiness and bizarre effect of making spirits flee at his presence made the bunny a source of light for the smaller creatures in Fluttershy's care, but he was just a small bunny, after all.
Pinkie's family was almost entirely subsumed into a single mass of stone and outstretched rotting flesh, and only her father made it out alive, although both have since lost their splendor and wander the world aimlessly, glad that they at least still had each other.
Applejack's family was safe on the farm thanks to the insane amount of spirits swirling about the premises protecting it from even the horrors that peered through the cracks in the sky. It ended up bringing in outside ponies and creating a small community of farmers and harvesters which brought the foundation of the village of Applevinegar with it with Granny Smith as its head before Big Mac took over.
Rarity vanished from sight, becoming yet another missing casualty in the world under the shade of the Green Sun. Whether she was caught by the dead, took her own life, fell to some horrid event, or simply left the known world would forever be unknown.
Rainbow Dash became the first mare to guide the pegasi to better lives higher in the skies. With the magic from her element, it slowly began to mutate the pegasi into a brand new breed of pony, one that was exceptionally fast and able to breathe easily despite being in low orbit. Their sleek and smooth forms terrified the survivors of the world which confused them for hellish monstrosities like the rest. It would take time to be accepted in a world gripped by terror.
As for Moon Dancer, she poured herself into the studies of forgotten magic, intent on undoing everything Twilight had caused and refusing to stoop to the level that she had gone to. The greatest wizards of the past, be they pony or not, always utilized standard magic and even created hundreds of their own spells and schools of magic. There was no reason that Moon Dancer couldn't do the same.
The unicorn sat in a home dug into a mountain and peered through a reinforced window toward Canterlot. The sky was the most turbulent above the mountain: Swirling, cracking, crumbling, and wrapping over itself into a solid shape again before the events repeated. She was stuck in this refuge, helping maintain the wards that kept the spirits and undead out and hid them all from the prying eyes of the ones beyond.
Moon got back to transcribing old runes from old texts in her small room and sighed, relaxing. All things considered, this wasn't a bad life for her. She had regular food, was able to train her magic, and was given everything she needed to try and solve the world's problems. The mare had helped to create new, easier wards and spells that helped with growing food even with such a dark and infertile soil the survivors plucked from the outside.
Still, this wasn't a way to live. Moon Dancer needed to help get the ponies and other creatures out of the predicament they had found themselves in and quickly rushed to work. As she listened to the head of her quill scribble ink into the parchment, a thought occurred to her: Was this what Twilight felt like with Princess Celestia? Utterly consumed by her self-assigned purpose that nothing else mattered.
Moon would have to make sure this thought was always at the forefront of her mind, lest she fall into the same despair as her former friend.
In the end, she was lost, like everypony else, hoping for a better future and being disappointed when they woke up to see everything got worse. A lesson in tedium that brought more despondence to the survivors. They kept themselves occupied by digging tunnels deep underground and joining up with other refugees, much to their surprise. Everything gradually started to grow into a small society in the darkness below and ponies were grateful, but then came the non-ponies, and with the need for survival, tensions rose among the refugees, even among their fellow kin.
Everything was getting both worse and better as time went on, but the world hadn't died. Moon believed it had just been temporarily occupied.
The unicorn once again found herself looking at the castle, thinking about what became of Twilight when those rectangles changed the essence of the magic of harmony and infused it into her. Moon hoped that the mare died, making it easy to take out Celestia when they got through. Unfortunately, because the pale unicorn was one of the 'normal' ponies that didn't study forbidden magic, Moon Dancer had no idea that all of this would have instantly ended had the lavender unicorn died.
Twilight had survived the ordeal she was put through and came out significantly stronger. Boney wings coated in a membrane of purple magic had grown from her back and left a trail of purple, white, and gray sparks wherever she went. Her body had grown tall and bony as her magic surged from her hooves, mane, and tail. A thick, sparkling mane and tail dragged behind her as she walked, as though she were in the water. Her horn had grown long, but it had fractured in half and several parts of the surface were chipped. However, everything still stayed in its place, floating next to each other and impeding in no way Twilight's ability to use magic. Her eyes had grown dark with the magic coursing through her, leaving only her iris of bright violet burning like rings of fire as she gazed at Celestia in glee.
The former princess of Equestria was fully a skeleton consumed by the green fires. They imitated the way the alicorn looked like as they burned and often flickered away, leaving behind the burning skeleton. Twilight didn't register such a thing, addled and shattered as her mind was, and she just hopped about happily, often having 'conversations' with the former princess.
Spike hadn't moved since the day of the Green Sun, watching the mare bounce giddily around the corpse of Celestia and awaiting an order. The only thing left of Twilight's mind was her love for Celestia and the tremendous smile she bore at all times while dancing around her body and the throne, trapped in her illusions of a filly being praised by her hero, mentor, and beloved teacher.