The empire was not the one to discover them. Kind jedi found the small planet of Equestria in a secluded portion of the transitory mists, a portion of the galaxy that is difficult to traverse and home to the Hapan Consortium, a kingdom built by pirates. In the system were various planets, all rich in minerals and gasses that the rest of the galaxy would make large profits from if given the chance. The jedi however feared what might happen if the world was made known to the galaxy, especially since a sith apprentice was recently found and defeated. So, they came up with a different plan.
Landing on the planet, the jedi were surprised for various reasons. First, there was a lack of fear amongst the indigenous race. The populace had only just reached the farthest planet in their system and had a budding space port, and yet they reacted to the jedi and their ships with curiosity and kindness, a reaction unlike any the jedi had read of prior. The many faces, and the bodies attached, were close to those of humans except that they were covered in fur, had equine ears, furry tails, and hooves for feet.
Then came the second realization for the jedi. The “ponies” ,as they chose to refer to themselves as, came in four variations, and each of these variations came in every shape and color. Having found this place while on a secret mission, no one came looking for the jedi as they overcame the language boundaries and became acquainted with the different races amongst the ponies.
First, there were the unicorns. They seemed to be the race that led in the intellectual endeavors of the race, although there were exceptions. The most remarkable characteristic was that they could all use telekinesis and others had more powerful abilities. One was brought in with the specific ability to link minds with others but without the ability to read memories or invade. The jedi thought that they had found a race that produced force users by the hundreds, but most were far more limited and lacked the force sensitivity of someone who could become a jedi.
Unicorns, with their glowing horns, weren’t the only race here that shined particularly brightly in the force though. Pegasi, a winged race that flew through the skies, were quite the oddity to the jedi. The wings weren’t the right size, the air sacs inside them weren’t big enough, and they weighed too much for flight to be possible. Yet, day after day, the jedi watched them take flight. They rejoiced in the freedom their flight offered them and watching their worry free flying made it hard for the jedi who stayed there to want to go home.
Even the ones they called earth ponies, the ones with no horns and no wings, seemed to have more of a presence. They tended to the lands and seemed to have slightly higher strength and stamina than their fellows, traits that could go exponentially farther as well. The three races lived in harmony; no pony felt constricted or restrained by what race they were born into. There wasn’t even any hate or prejudice that so many other worlds had showcased to the galaxy.
The perfect example of this were the rulers. Only a few days after the jedi’s arrival a handful of beautiful, graceful figures approached. Each had not only a horn but a pair of wings as well, and a very proficient use of both. A royal class, these alicorns showed how accepting and kind the race could be, never once fearing the jedi for what they were. It was from amongst this race that the first of the Equestrian jedi came.
As the years passed and more and more civilian minds were placed in danger by the sith war against the old republic, the jedi who had stayed there returned to the rest of the galaxy. While they kept the location of the planet secret they snuck engineers, doctors, and scientists in ones and twos to help the Equestrians continue their accelerated pace towards catching up to the rest of the galaxy. Finally smugglers who wore armor, Equestrians in disguise, took over for the jedi by offering safe haven for the persecuted as the jedi all went off to war, leaving their apprentices and the one Equestrian master to their own devices. The planet as a whole weeped at the horror that was order 66.
The empire rose and it was from those they brought to the small planet the Equestrians learned of the danger the sith and their plans. For the first time ever, the four races united, focused on preparation for an incoming war rather than their normal co-existence. After many years of expecting a vicious assault, it finally came and the empire was very surprised by what they found. The newly built star destroyers, frigates, cruisers, and even X-wings crushed the small exploratory force that had tripped upon the new system. The empire, still dealing with the height of the Rebel Alliance’s power, waged a small war in the system. However, they used far fewer resources than was required. The Equestrian losses were far higher than any other commander would have allowed to happen, with their lack of military experience showing through.
That was when one of the smugglers, an alicorn who refused to sit around ruling, hired the mandalorians. Under the guidance of the mandalorians, the Equestrian forces crushed the much smaller imperial force, and the Equestrians learned what it meant to have true allies in the galaxy. When Palpatine finally fell and the Rebel Alliance became the New Republic the Equestrians came in, providing relief, helping mop up the imperials, and establishing themselves as a kind and harmonious force in the newly settling galaxy. Thus, the Equestrians spread to the rest of the galaxy and helped re-establish the jedi order, lore, knowledge, and training, having been maintained by the jedi order that had independently survived through all of this.
-Final historical summary of the discovery and growth of the planet Equestria and the Harmony System