The Elements of Harmony are known as one of the most powerful sources of magic in all of Equestria. The Elements of Harmony were birthed from the Tree of Harmony, a mysterious and magical tree found by Luna and Celestia who used the elements to stop Discord and save Equestria. Though the Tree of Harmony has used it's power to save Equeastria more than once, many questions about it are left unanswered.
Where did it come from? How long had it been there? What pony planted it and why? While it did indeed use its powers to protect Equestria, the Tree of Harmony was created to serve as the will of a God.
Before the existence of magic was discovered, the land which had yet to be Equestria was torn apart by a seemingly never ending war. Earth ponies, unicorns, and pegasi alike all fought for dominance over the land. The princess ruling at this grim point in time was a young earth pony named Genesis De Magia. Genesis had tried her hardest to resolve the conflict between all the tribes with peace countless times as she despised violence and saw the war as senseless fighting which she knew no side would win, however, every attempt she made only ended with the same resulting failure.
After many years of her subjects suffering, Genesis decided what had to be done. Deep down at the bottom of a ravine were no pony dared venture, grew a unique tree known at the time as the Seraph Tree. The tree was seen as a very important deity figure and was worshipped by all who knew of it, however, it was what was on the tree which gave it such a sacred reputation. On the tree grew a single strange berry unlike none ever seen and it was considered forbidden by all that no pony should even let the thought of touching it slip their mind.
Yearning for a peace that she feared would never come, Genesis ventured forth to the tree and consumed the berry which granted her Godlike magic as well as a sharp unicorn horn and a pair of large white angelic wings. Using her newly endowed magic abilities, Genesis solely ended the long running war and was worshipped as a Goddess for her deed as well as for being the first Alicorn in history. She returned back to her kingdom were she began to teach others about magic, though she discovered only unicorns could utilize her teachings. She eventually fell in love with a colt unicorn who was a student of her's who was in the same age group, and together they conceived a young pony whom they were happy to call their son.
Though as time went on, Genesis began losing trust in the other ponies and due to her now higher state of being, she became corrupt and convinced herself that the unicorns she taught magic to would now attempt another war. After succumbing to madness out of fear that another war would break out and more lives would be lost, Genesis used her divine powers to move the moon in front of the sun, blocking its light from hitting the earth. As the darkest side of the moon consumed the sky, darkness fell across the land and all who were caught in it's gaze fell under the Goddess's spell which drained their spirit, color and even their distinguishing features. Pegasi lost wings, unicorns their horns; allowing the goddess to control everypony within the shadow as she pleased.
Within in the few short years it took him to grow, Genesis noticed that her child now wielded a godlike magic very similar to her own. Genesis raised the young unicorn in the ways of a God, teaching him that they are above all others and attempted to convince the unicorn that her eclipse was necessary to maintain peace. After watching the other ponies for a few years, Star Swirl was convinced that this was not true peace for no pony was happy. In a attempt to change the fate of the land, he tried talking to his mother about her “peace”. Seeing she would not listen to reason, Star Swirl challenged his mother and fought for all ponies.
He was victorious and even managed to undo the eclipse that she had created, however, with the power of a god coursing through her very being, Star Swirl couldn't completely defeat his mother. Instead, he used his own divine powers to seal her within the Seraph Tree and banished it to the darkest side of the moon where it would be unseen and forgotten by all. When the Seraph Tree was removed a strange new tree sprouted in it's place, Star Swirl claimed that it represented the unity and good of all ponies and their newfound peace; and with that, the Tree of Harmony was born.
Star Swirl eventually went on to better hone his own abilities and learn more about the newfound magic element which his mother had left behind. He became known by many for his knowledge and even went on to teach many other unicorns magic as well, and though his divine magic over time became more of an old myth than factual, Star Swirl still knew what he was capable of. He rejected the life of a deity fearing he would turn as his mother once did, and instead, settled in life as a unicorn and covered up anything in his past which could lead to others knowing of his powers.
With the wicked goddess sealed within the penumbra of the darkest side of the moon and harmony restored to the land, everything had seemed at ease. However, deep within the soil of where the Tree of Harmony had sprouted, roots from the Seraph Tree still remained which carried fragments of Genesis' will inside. Over the years it had grown the roots of both trees became intertwined and began to fuse, producing some of Genesis's will inside the Tree of Harmony which began to consume its magic from within. On that day, the Tree of Harmony not only served as the beginning of a new start for the land, but also the beginning of a god's rebirth.