The following story takes place in a slightly alternate timeline, inspired by the Crystal Empire future in the season five finale "The Cutie Re-mark". The action happens at the beginning of season three, replacing the events in the two-part episode "The Crystal Empire". All events which occurred in the series prior to that episode (such as the wedding of Shining Armor and Princess Cadance, Twilight still being a unicorn etc.) are unaltered.
It had returned!
Out of thin air, the Crystal Empire had reappeared into the world, after having disappeared for more than one thousand years.
Seeing an opportunity to help its inhabitants, the crystal ponies, Princess Celestia sent the newlywed couple of Princess Cadance and Shining Armor to assist them. They quickly took charge, vowing to protect the land from all evil and to find the Crystal Heart, the magical relic which stood as a symbol of hope and security for the entire realm.
However, there was one more thing that reemerged along with the Crystal Empire … out of the shadow realm King Sombra had returned. His dark powers, fueled by the despair and suffering of other ponies, were at their peak, as was his determination to take back his position as absolute monarch of the domain.
Despite Cadance's effort to shield the realm in a force-field in order to prevent the king's malefic influence from spreading, Sombra's power was too great, his umbrum magic easily penetrating the barrier and entering the confines of the newly appeared land. Terror and sorrow filled the hearts of the crystal ponies upon seeing the tyrant had returned, which strengthened the foul king's sorcery, allowing him to take physical form and regain control of the empire.
Knowing they were too weak to compete with the sinister unicorn, Cadance and Shining Armor managed to quickly rally the few crystal ponies who managed to resist Sombra's corruption and flee to the frozen lands in the north, but not before taking with them the one artifact which the oppressor assumed was too well hidden to be found - the Crystal Heart.
Once he assumed power, it didn't take long for Sombra's ambition to grow, so he decided to turn his newly re-acquired slaves into soldiers and start a war with Equestria. In what seemed like mere moments, wave after wave of crystal ponies clad in dark armor, with spiked helmets and sharp weapons descended upon the once peaceful mares and stallions ruled by the princesses of the Sun and the Moon. The war helped disseminate fear and misery throughout the land, increasing the king's dark powers, who used his magic to spread the black crystals and the cold of the frozen north throughout his newly conquered territories.
Despite both Celestia and Luna leading their troops, often from the front lines, and in spite of Princess Cadance and Shining Armor keeping up a resistance front in the north, the malefic tyrant seemed to have the upper hoof in the conflict and it took every single pony in Equestria working hard day and night to keep the war effort going.
Everypony's life had changed for the worse, and although the ongoing struggle took its toll upon their lives as well, for six particular ponies, the most horrific moments of this event were yet to come …