After the invasion of Canterlot in 2500PU (Post-unification of the three tribes) Equestria began to decline as a nation. As people learnt of how changelings could easily hide amongst society, they became afraid, very afraid bordering even on paranoia. Sadly it was foreigners such as griffins, Minotaur’s and zebras that were treated the worst, as they were slowly forced out of society, hidden away at the fringes of towns and cities, their goods being boycotted and as a nation, Equestria started looking inwards becoming more racist and xenophobic straining ties with foreign powers. When the princesses and the element bearers stepped forward to try and encourage social harmony and acceptance of other races, they were shunned and ignored as rumours began to spread of them secretly being changelings. Rumours that spread to every corner and every part of society. Eventually leading to the princesses being forced further and further away from their legal duties and decision making as the nobility of Canterlot lost faith in the princesses.
By 2510PU they had no political power being completely impotent and unable to prevent the numerous decrees that forced non Equestrians further and further away. This in turn lead to disdain and spite from other nations, who began to cut ties with Equestria, breaking alliances and trade agreements until Equestria was alone. Then there was the nail in the coffin. In 2515PU a decree ordered that 'every being of non-Equestrian origin or non-pony species is hereby immediately arrested and jailed to either be arrested or in case of potential threats executed' the princesses to were neutralised and arrested in their sleep, equipped with anti-magic fields and rings as well as chains of the toughest, strongest steel and orichalcum. Twilight sparkle and the element bearers suffered a similar fate, forced into reeducation camps. They would later be freed after 13 years imprisonment. To house all of these new prisoners the crystal empire was changed from a city to a humongous prison, otherwise known as the “Tower of Latria” because of it's isolated and inhospitable conditions no one ever escaped alive, and it was designed by two near identical brothers as its architects.
These actions irreversibly damaged and split society, and lead to a civil war beginning in 2516PU as well as a war with the Griffonian empire beginning in the last month of 2515PU. This was the beginning of the end for Equestria as a free and liberal nation and lead to 12 years of bloody tumultuous war. On one side was the Equestrian government leading the royal guard and their vassal the crystal empire with generals such as Shining Armour and Blueblood who disappeared about a year or two into the war as a deserter and never found again. On the other side was the rebels supported by the Griffonian Empire armies led by ponies such as Starlight Glimmer, and Braeburn.
Early on in the war the army discovered what remained of the Changelings forces in a network of caverns in and around Froggy bottom bog and ghastly gorge, enslaved them and forced them back to Canterlot along with Chrysalis as slaves to run the mines and sweep the streets. Without them the slime of the caverns and tunnels decayed turning into a rotten and putrid mess highly poisonous to all who entered, as well as being magically volatile twisting and changing the landscape after it became a dumping ground for magical waste and experiments during the war.
It was on the dawn of the longest day in the year 2521PU that scholars in the crystal empire found out about the legendary soul arts of myth. Battle magic’s of great and incredible power that could be used more often and cast faster with more power than the battle spells of rudimentary magic, as well as wieldable by any living sentient being with practice and knowledge. It revolutionised warfare on a scale never seen before, and the death toll skyrocketed as the government pushed the rebels back slowly with their new power, the troops of the Griffonian Empire were also forced further back as well until six years later they were forced out of the country and the rebels exiled to froggy bottom bog and ghastly gorge on the border of the Everfree forest and then locked in by a roof and walls of dirt and earth sealing them away forever. But still they magically dumped all their waste and all things unwanted into it turning it into a valley of defilement a home to the lost and wretched.
When the war ended Equestria was a blasted wasteland barely keeping itself together as the population was decimated from the war, so the government consolidated its power building vast fortresses and castles in and around Equestria most notably one on the railroad leading to Canterlot turning it from a simple road to a near impenetrable gate impervious to magic and physical force via hundreds of intertwined enchantments and seals. Another famous one was the fort between Equestria and Griffonia manned by a thousand soldiers armed and trained for war at all times.
With their wills completely broken the element bearers were released, Rainbow dash forcibly conscripted into the army and forced to man the prison at Latria, Applejack returned to her farm and began to rebuild, Rarity became the court dressmaker and was no more than a slave to the courts whims dissapearing soon after never to be seen again. Twilight was forced to join an archaeological expedition to an ancient Minotaur ritual site on islands just off Equestria’s north eastern coast and become a researcher on these new magic’s with Moondancer as her apprentice, while Pinkie Pie was forced into servitude and sold to the diamond dogs as a slave. This removed a potential threat to the leaders of the country except for Fluttershy. Her selflessness, kindness and caring motherly nature caught the church’s eye.
The church having risen to prominence during the war declared that there is a god upon the discovery of the soul arts, after all if no afterlife exists why do we exist? And as the soul arts prove the existence of the soul, the fact they can be used by certain ponies to heal wounds and even resurrect the dead means there must be a benevolent being up above who cares about us, thus there must be a god. As the war raged across Equestria, many turned to this new faith for comfort and reassurance and thus did the church come into being. Volunteers formed a militia, that eventually grew into a knightly order to protect the church and six saints were chosen all of whom had found relics of great and sacred power intrinsically linked to the powers of the soul arts, one of whom was Fluttershy and she was brought out of the prison to become the sixth saint of the church.
She soon went on pilgrimage to the valley of defilement three years later, taking three holy knights with her, Istarelle who wielded the lance of god, Vito of the moonlight blade and Iron will her bodyguard, the bane of magic. In an attempt to reform and redeem the people of that vast swamp, but they never returned. Most assumed they had been killed, but they forgot about them as the year after that the Princesses disappeared from their cell, and no trace was ever found of them until the year after that.
They never found princess Celestia, but they definitely found princess Luna, or more accurately Nightmare moon, leading a wave of demons across Equestria killing all enemies in their path and eventually reaching and conquering Canterlot destroying all lines of defence in a single day and consuming the entirety of Equestria as well even the great border fortresses. In the north the crystal empires leader Princess Cadance was overthrown, and her daughter flurry heart slain by more demons who conquered the city and forced it’s people into the prison under the commands of one known as the old monk.
The tunnel kingdom of the Diamond dogs was also consumed by the fog too but stopped at the borders of the crystal empire, Equestria and the diamond dog’s lands. When the demons marched further north into YakYakistan, their advance was stopped as they were defeated and forced to bunker down in the deep fog that now slowly creeps across the world promising a slow but steady extinction to all life. However other nations were ignorant of the true cause of the deep fog and only learnt the truth after a survivor managed to flee the fog.
They told the world of how someone or something had awoken a being known as the old one, a slumbering beast that lurked at the heart of the world in the Nexus, and how the colourless fog brought with it a seemingly unending tide of soul stealing demons who drove men mad attacking any who still had a soul as they now desperately craved what they now lacked. The mad attack the sane and chaos reigns while the demons grow stronger as they feed upon their victims souls. Whoever killed a demon would earn that power, a power beyond human imagination.
Mighty warriors entered the fog either to save Equestria or to become powerful and mighty beings, But none of them ever returned. The twin bodyguards of the griffin emperor Biorr and Vallarfax, the 4th saint Jet set, a wandering cleric. Garble the silent lord, Patches the hyena and the wanderer Scirvir. Now no one dares to cross the fog, and it slowly creeps across the world unopposed.
But there is one final light in this dark tunnel, Gilda has been thrown into the fog as an execution method for stealing food from the kitchens of the great Griffon Emperor. Now the only hope for the entire world has Equestria found it's saviour or the demons a new slave.