"Four thousand years ago, the Great Equestrian Civil War (28 B.D - 1 B.D) broke out between the three pony tribes: unicorns, earth ponies and pegasi. Many historians in the past and present argue about the original reason for the war, but it is widely accepted that the three tribes were fighting for the land now known as Equestria. It is estimated that millions of ponies had lost their lives during the war, including the legendary unicorn general, General (once Princess) Platinum (45 B.D - 22 B.D), and her son, Obsidian (24 B.D - 22 B.D), who both perished in the Northern Raid of Unicornia. At the end of the war, the damage to the once-pristine lands was extremely substantial, as most of the lands were either sealed in permafrost or too damaged to settle into by the time the unicorns won.
The war is still known as the first and bloodiest in Equestrian history.
Apparently, the unicorns were led into the war by Princess Celestia herself, Lady of the Solar Throne. Her Highness ensured the tactical victory of the unicorns, managing to conquer the Equestrian mainlands from the earth pony armies and thoroughly flushing out the pegasi from the Everfree. As soon as the other tribes had surrendered themselves to the unicorns, an agreement was settled upon: the unicorns would occupy the mainlands, the earth ponies would either submit to the unicorns as labourers or be driven to the outskirts, and the pegasi would be forced into finding new lands beyond Equestria.
But through the many years, the reign of the unicorns experienced many an enemy to the throne, threats from both beyond and within Equestria, ranging from an attack from Queen Chrysalis's Hive to the Earth/Lunar Rebellions lead by a magical entity, The Nightmare (once Luna). A solution was found for these threats, in the form of the Tree of Harmony and its gifts: the Elements of Harmony. However, the gemstones, though filled with extraordinary magic, were unable to do anything of much use.
Fortunately, by the usage of advanced wartime spells, the elements were tricked into forming a continuous harmonic barrier around Equestria and the surrounding Pegasian Wilds. With the Barrier, every threat to the throne had been banished from Equestria. However, not much is known about the fate of the Nightmare, aside from the fact that she was not banished beyond Equestria or to the moon (Contrary to popular belief).
At last, Equestria can experience a long age of harmony to come."
-An excerpt from Segregated Equestria: A History.
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Yeah, right. If only they knew the truth...