After taking planet Earth from humans in an alternate reality, all ponies were ruled by Sombra's father, the Unicorn King, who was one of the more...radical pony revolutionaries. He was a cruel and merciless tyrant, making the entire economy revolve around him, which of course upset the balance for everyone else, causing them to all blame each other and hate each other, allowing Windigos to feed off of them and "defacate" cold air, freezing the land.

Starswirl, who had good intentions but utilized Machiavellian ways to achieve them, was determined to sabotage the Unicorn King's rule and make all the "delegates" see eye-to-eye, and make them aware that their positions were, contrary to what they thought, meaningless titles to distract Ponies from knowing the actual nature of their government. So he did a rather demonic summoning, which somehow resulted in the fusion of himself, Platinum, Hurricane, and Puddinghead, and then fused them with raw entropy and the raw material of the Universe (these two different things have both been associated with the concept of "chaos") as so Discord was born! With the raw drive from Starswirl to incite rebellion against the Unicorn King, the monstrosity became a complete anarchist.

Celestia, Starswirl's apprentice and secret lover, sought to finish her lover's work and transmute herself in an Alicorn in his stead to overthrow the Unicorn King, and then imprison Discord. Like Cyrus the Great of Persia, she overthrew the original King and laws, but spared the Unicorn governors and re-adjusted the laws to be more fair for all Ponies. The origins of Celestia and Luna are rather mysterious and nopony is sure who they were and where they came from. All that Celestia has revealed was that she was a Unicorn apprentice to Starswirl and she and her sisters became Alicorns and used their new powers to protect the defenseless from predators. The bit about being Starswirl's lover was a bit of information that Celestia revealed to Twilight to prevent Twilight from being as perpetually heartbroken as herself. Celestia may or may not have been Clover, and if not, was likely her friend, or perhaps her rival, similar to how Twilight and Sunset Shimmer would have certainly been rivals had they met sooner. It's also possible that Celestia would rather forget who she was before, if she was anyone before.

One of the regional governors who served the Unicorn King was actually the grandmother of Chrysalis, and none other than the Princess mentioned in the "Love" poison story: She had lust-poison-born child, who was a mutation and monstrosity, and rejected from her home, considered best left forgotten. However, against her knowledge, this proto-changeling had bred with other oddball creatures in Equestria, who were considered below the Earth Pony-class until Celestia fixed everything...among the targets were Driftwood-Changelings and Flutterponies, and as they became increasingly separate from the rest of Pony society and increasingly prone to nomadism and self-governance, they soon became their own empire in caverns on the outskirts, almost entirely under the very nose of first the Unicorn King and later Celestia. Unfortunately, as nearly all of them had a little bit of the Lust-Poison blood in them, they all were physically, mentally, and even emotionally rotting parasites whose constant rotting resulted in leprous legs with holes in them! This Lust-Poison influence also caused them to be inevitably selfish, callous, dishonest, arrogant, and greedy, even if not especially hateful and vengeful, and certainly not beyond hope of repentance for some individuals. But like the Skeksis, they have no qualms over trodding over other species to ensure their betterment, and only have a few mild qualms about trampling over each other. As they are a very new race and not numerous, they usually fight by guerrilla warfare and sabotage, hence the elaborate plan to invade Canterlot from the inside. However, they still have been around for over a thousand years, so most of them have become very un-pony and very much like Driftwood creatures: Chrysalis is an unusually old specimen who has a lot of Pony inside her, as she is literally the daughter of the first Lust-Poison corrupted Pony, hence her more equine appearance and Alicorn properties, which slow down her aging (but not her decay). So, basically, the Changeling Empress is the child of a Unicorn Princess, making her daughter Chrysalis the granddaughter of this Unicorn Princess.

King Sombra was also a regional govener, firstborn son of the Unicorn King, and one of his scant few children to actually be valued in any way by him and thus given a job of actual power rather than one to distract like Platinum had. Sombra dealt with his frustrations of the possibility of never getting the throne due to his father's quest for immortality on the people of the Crystal City he was sent to govern. When his father was out of the picture, he threatened to use the Crystal City as the antenna of his dark magic to take over Equestria. Letting his threat be public and spread far and wide was a very bad move, as it drew the attention of the new Princesses of Equestria, who brought a large army and threw him out of his city, threatening his execution should he ever return. Needless to say, Sombra must have felt more than slightly foolish after that, and must have hoped that cursing the Crystal city would help him in some way.

Before the Unicorn King ruined everything, the Crystal City was it's own separate country, and Cadence is a direct descendant of the original rulers of the region before the Unicorn King took over.

There is also a separate ethnicity of equines, the Przewalski's Horses, who tried to conquer the ponies and make them their own before all of these events even happened. The invasion was repelled, the battle made it easier for the Unicorn King to take over, and the Przewalski's Horses left Equestria well alone for 2000 years afterwards, and when they resumed relations with them, they were far more friendly.

That's just part one, eplaining the basics of why everything is the way it is, I'll post a basic timeline later on this thread!

Wow. I didn't read all of that, but you sure have put a lot of thought into this! My own headcanon backstory is pretty convoluted, lol.

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Thanks!