Based on Monsterverse-Apophis by ToonHolt
 
In the beginning, there was nothing. A void of Darkness. A cold eternity of silence. And all have come to the same conclusion: that life could not have possibly existed before our own. And in the end, all of them are wrong. For there was ONE being in all of the Harmoniaverse who once dwelled and ruled over the emptiness as its sole occupant. His endless, and expansive coils slithering throughout the dark expansion, and relishing in the Darkness he reigned within.
 
His name was Apophis, The Primordial Elder-God of Darkness and Anarchy.
 
But Darkness is not as eternal as many believe. And The Source decreed that the time of Harmony, and Light was due to come forth. In order to bring these forces into unified existence, and ensure that light exists alongside the darkness, a sacred tree was forged. That tree would one day come to be known as Lignum Harmonia: The Sacred Pillar of Harmony, and Light. For within this mystical monument of shimmering crystal, and diamond -like sheen, came the suns and stars themselves. Spreading like podlings to fertilize an empty field, and fill it with life. That is how many worlds came to be, and how they were all born with the essence of Magic, itself.
 
But Apophis hated this accursed Tree, and how its infernal Light corrupted his perfect void. So much so he desired only its destruction, and death of all connected to it. And many times he would seek to undo Lignum Harmonia in the hopes of killing harmonious elements it birthed, and the light that originated from it. Cut off the head of the beast, and it will die. But The Source did not leave this sacred lifeform unprotected. Born into creation alongside the sacred tree came the Bahamut: a race of lesser Elder Gods who embody the earthly aspects of existence. And those that protected the tree were known as the Archangels. And even with all his control over Darkness, Apophis could never hope to overcome so many lights at once. Alone, he could accomplish nothing. But, looking back upon the many races of Bahamut outside the Archangels, who embody Light, he realized that perhaps he could take advantage of such numbers, and begin producing an army of his own. And after practicing on mortals for eons, he inevitably came to realize that even Bahamut were susceptible to that most evil element of all: Corruption.
 
That is how the Third race, after Bahamut and then Mortals in that order, was born: The Elder Gods of Darkness, The Djinn.
 
With every soul corrupted by evil, and Anarchy, Apophis’ power grew. And when his power rose to its zenith, he himself was able to take the form of his enemies, and became a Primal Djinn in the dragonian form of a Bahamut. A war then waged for the existence of Light, and brought calamity to many worlds. Many Bahamut, and many Djinn fell to this cursed war as Apophis struck blow, after blow to accomplish his mission. But even though he had conquered the ancient city guarding the dimensional gateway to Lignum Harmonia, he still found himself thwarted by a nameless Bahamut, who had been chosen to become the sacred tree’s Champion of Harmony, and Light. With the aid of her close allies, Apophis was laid bare, and struck down by the very power he sought to destroy. But the dark cobra was as cunning as he was heartless. As his body vanished into the nothingness of oblivion, he bellowed a final order to his mightiest of Djinn, The Balrogs. And together, they channeled the full powers of Entropy, and destruction to end the universe itself. If Apophis could not live to rule a world of darkness, then he would ensure none would outlive him. His plan had nearly payed off, as his Entropic Erasure Orb saw the universe consumed by nothingness, and compress into itself, while taking every Bahamut and Djinn, and mortal with it, along with seemingly all of reality.
 
But Apophis underestimated the power of Lignum Harmonia. And while his doomsday attack did see to the end of one universe, the all-powerful conduit of The Source altered the essence of the attack to ensure that after destruction would come creation. Thus the universe would be reborn, and would thrive once again as it had before. As for the Bahamut: though they too died in this calamity, they were beyond the mortal concepts of death. So long as the elements they embody exist, so too do they. And in time, they would slowly but surely rise once again as Mina Mor’Caeli - the Sentinel City - had been restored following its destruction, and taken to a new world where few would think to look. And thus, the sacred tree, and the Light and Harmony of existence remained alive, and well.
 
Unfortunately, as long as there is Light, there will always be Darkness. And although he had indeed perished in the great calamity, his spirit endured with the Darkness. A weak, and frail thing that found himself in a realm where Darkness reigned supreme. From here, he would regain his power over the eons. And in the process, he would continue his grand mission to return the worlds to Darkness. The Djinn had long become extinct, with only him remaining, but he would have no problems finding suitable pawns to aid in his restoration, and return to power. At first, he thought he had found it in the form of the Bahamut of Darkness, Grogar, whom he subtly influenced as anger, and hate began to control him. But he proved unsuitable for Apophis’ needs, and was left to his own end - though at the cost of Apophis’ essence, which had left the realm of Darkness to inhabit Grogar as a silent passenger until he was strong enough to claim the body for himself, was imprisoned in the very Bell he had influenced Grogar into making: Belial’s Maw. Yet even from inside the bell, he influenced the world of young Equestria, and corrupted many different souls in order to find the one he needed. By his will did many of the terrible events of Equestria’s history come to pass. All so that he may find the one who would not only free him: but also who could bond with him in mind, body, and soul to create a new Primordial Elder God of Darkness.
 
And to the dread of the universe, Lord Tirek may just be the host he had been searching for.
 
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Yep. This is the source of every bad thing that’s ever happened in the Harmoniaverse’s Equestria. The underutilized, and underrated God of Darkness in Egyptian Mythology is now the Vaatu and Brainiac DCAU of My Little Pony. And Lord Tirek is Unalaq and Lex Luthor in terms of symbiotic relationships. This snake is the one who’s been teaching Tirek everything he knows about the Dark Side, and how to utilize his evil powers to the fullest. The centaur’s ultimate endgame will be to unleash the Elder God upon Equestria, and merge with him to be reborn as The Supreme Lord of Darkness.
 
And woe betide any who would seek to thwart him.
 
(I wonder if i’m unwittingly taking a hint from Sir-Writesalot when it comes to this concept, including Tirek ultimately being what basically equates to the Avatar of Darkness?)