I started jotting this down a while back and thought I'd share some of it.
Our setting: the world that will come to bear the name Eternia. Rising from the primordial ooze into sapience, its original inhabitants are a race of saurian humanoids calling themselves the Lloigor.1 Around the same time a second reptilian race — naming themselves the Kaa2 — achieves sapience, the Lloigor discover magic; this discovery eventually leads the Lloigor to become entities whose name will be translated into the human tongue as 'dragon'.3 Largely abandoning physical form, many dragons eventually travel out into the universe and other planes of existence; those who remain either retreat into the dream realms or rise to godhood over their evolutionary cousins. The dreams of the slumbering dragons have profound effects on those Kaa unfortunate enough to settle near them; those of the godling Dagon for instance mutate one such group into a race of mer-people.4
One of the transcended Lloigor explorers eventually encounters an immeasurably ancient entity named Thoglys who in later ages becomes known more simply as the Horde.5 Hideously corrupted into the Horde's avatar and taking the name Hordak, it leads the entity back to Eternia where they arrive unremarked at the height of the Kaa culture. The entity spreads like a cancer, twisting or destroying everything it comes into contact with. Most resist, many die horribly. Others instead come to worship its dire presence, giving themselves to it willingly and surviving... after a fashion.6
The effort to expel the entity and its worshippers back into the outer dimensions is ultimately successful, but the Kaa are left shattered and facing extinction — as a final act of spite, Hordak redirects a small planetoid from its path near the system's sun, setting it on a course that will make the planet uninhabitable for millennia. The survivors trust to their science and seal themselves in the deepest caverns, there to hibernate until their guardian systems tell them that the world has healed itself in the wake of the apocalypse.7 Ironically there isn't one, as the dragons join their power so that the planetoid shifts into a highly unusual orbit, becoming the planet's third moon; it only ever illuminates the same half of the planet at night while the other half sees it only as a well of darkness against the stars.
Countless years pass.
The expulsion of the Horde had left a cosmic fault-line; crossing the wake of the fault's movement, the human colony ship Eternal is flung through time and space into the star system. Badly damaged, missing its sister ship and unable to return home, the ship's crew has little choice but to settle and partially terraform a ravaged world upon which they discover the ruins and artefacts of an alien civilisation. A capitol, named for the ship, is established in one of the most intact ruins. Abandoned lore and chance encounters with dragons pursuing their own ends leads to the settlers learning the sorcerous arts.
As the centuries pass, humanity spreads across the world it has named Eternia. Once again the dreams of dragons affect nearby settlements and animal populations, shaping them into new species entirely. Advanced technology salvaged from the colony ship and recovered from the remnants of the indigenous civilisation has by now degraded, its upkeep as much unthinking ritual as science8 while in some instances sorcery has come to supplant it altogether. A celestial alignment around this time opens the fault-line enough to allow the Horde to once again steal upon the world, basing itself in the same mountain fortress it had originally occupied.
As before the cancer spreads, but it lacks the advantage of ignorance it had previously enjoyed - the dragons have trained humans in the arts of magic precisely for this moment (though the agendas behind their doing so are not always benign9), while the spawn of Dagon are woken from their ancient slumber and fight both sets of invaders. Again the Horde is driven from the world, the final battle seeing Hordak suffer a mortal wound as he slays the great dragon Shaitan10 whose titanic form falls upon and shatters the fortress that will come to bear the name Snake Mountain.11 With most of the underwater settlements of the mer-people in ruins, and the keepers of the ancient sciences of both races all but gone, the world descends into an age of barbarism and superstition.
Some echo of the evil remains however, keeping open the tiniest crack in the fault-line through which the Horde will inevitably return. Though grievously crippled by the battle that saw Shaitan slain, Greyskull — the most powerful of the few remaining dragons — manages to sense this. Unable to leave her redoubt she infuses a human sorceress with part of her consciousness, creating an avatar that will come to be known by the world at large as the Green Goddess.12
Centuries pass. Science and learning are slowly regained, leading to the desperate beginnings of a renaissance. Stories of the Horde become regarded mostly as legend, though Shaitan's corpse gives rise to a small but persistent serpent cult that foretells of the god's return. No one remembers that humans were latecomers to Eternia, or that most of the strange races now sharing the world were once a single race. The mermen have similarly forgotten their origins and their long trapped cousins but maintain a cold disdain towards the vast majority of surface dwellers; territorial skirmishes are far from unknown.
1. Every version of MotU has featured the Snake-men as an ancient and terrible threat sealed away in a prison dimension sometime in the mists of pre-history. I'm going with them as the original inhabitants of the planet, making them into something other than a scaly version of the Horde. Their character design will have elements of Egyptian and South American cultures (Aztecs, Mayans and such).
2. Named for the character in The Jungle Book, because Snakeman is really just dumb.
3. MotU has dragons in the original cartoon and the idea of them serves as a useful tool here. The Lloigor are Mythos entities composed of psychic energy that are known to taken dragon form and capable of supernatural feats that have an effect on surrounding mortals.
4. Yes, it's another Cthulhu reference (and a Doctor Who one; see below). There's going to be a few of them - the genesis of MotU lies in Robert E Howard's Conan the Barbarian, which is actually considered a part of the Cthulhu Mythos. But it's also a good way of explaining Eternia's cornucopia of sapient species in the series
5. Derived from Cynothoglys, a Great Old One, because its description as a formless mass with a single arm pretty much matches what we see of Horde Prime from the She-Ra cartoon.
6. Becoming part of the Horde isn't about simply signing on with the winning side. It's about having the force of will not to be sucked into a husk of your former self . There's also something of the Beast & its minions from the movie Krull intended here too: in this version, Horde troopers aren't going to be robots...
7. Similar circumstance, same trick attempted by the Earth's original sapient reptile inhabitants from the Pertwee story The Cave Monsters. Same outcome too: instead of destroying the atmosphere, the rogue planetoid prompting the plan becomes Earth's moon.
8. An idea used by many, I see this as something similar in feel to the Imperial tech cult of Warhammer 40K.
9. Some believe that the humans are little more than cannon fodder to be expended keeping the world safe for the return of its original inhabitants. Others feel that having failed to rise, the snake-men have surrendered their claim to Eternia.
10. An Islamic demon; the name was modified to Shai'Halud in Dune as the Fremen name for the sandworms.
11. A dark inversion of the events of the Battle of Camlan.
12. A character from what is termed Preternia, the distant past of the MoTU setting that basically looks like the classic snake-cowled Teela toy from the 80s with green skin. Here the name is the formal title for the character known more informally as The Sorceress, as visually the character will have a costume inspired by the South American god Quetzalcoatl, a winged snake with green feathers.