Okay, so I know there is some story to Minecraft, we can read the dialogue after killing the Enderdragon, so a "plot" already kind of exists.
But I had like this pretty neat idea so I'll share it because why not.
In the beginning, there were three Realms - the End, back then known as the Aether, the Overworld and the Nether. Each was inhabited by intelligent beings. The Aether was home to some long-forgotten race, known as the Aethermen, whose remnants are the Endermen - mere shadows of a once-great civilization. The Overworld was inhabited by Players and Villagers, first being great builders and explorers. The Nether homed a race of the Wither People, aggressive and fierce warriors.
The Aethermen were... distant. They didn't interact much with the other Realms, minding their own aetherial business. It is not known how they looked, but my impression is like the opposite of the Endermen - white skin, golden eyes. Their world was inhabited by all sorts of flying beings, possibly dragons as well. The Aethermen themselves could not fly but were capable of teleportation (an ability extant in the Endermen). They did, however, build flying ships and created wings, know as Elytra. They might have been quite powerful, but never felt the need to share it with the others. They might have appeared occasionally in the Overworld to seek some resources or knowledge.
Players and Villagers lived in a kind of harmony. Villagers weren't the greatest hunters, miners or builders, so they relied on the Players to get resources and shelters in return for the food they grew and items they crafted. Players also provided defense against the Wither People and other dangers, like creepers, who has been in the world since, like, always (the Iron Golem may be a later invention of the Villagers left without any Players to guard them or an independent invention all along; the Illagers appeared fairly recently, so they may be descendants of normal Villagers who played with necromancy or simply... changed as the world became more hostile). The Players would then be the ones who created mineshafts, ships and temples (this gives a lot of space for more of abandoned structures to be added in the future versions of the game; I did not consider the water temples so it's an open topic).
The Wither People were most of all, warriors and raiders. Using the obsidian portal, they entered the Overworld to attack and raid for resources or simply as a form of entertainment. They often waged wars against each other, too. The enslaving of Villagers and Players was attempted, numerously, but neither could withstand the barren conditions of the Nether and therefore, the Wither People created Pigmen, a race of slavers, modified so that they could survive in the Land of Fire (possibly an act of humiliation as well - the people being combined with pigs, animals farmed for meat, living in the dirt). Zombie pigmen are remnants of those slavers (the Wither People knew and used necromancy, so it would make sense). The blazes might simply be remaining guardians of the temples, so a creation of the Wither People as well. The Wither, now a boss, was back then a weapon of destruction, crafted with heads of their own people. How gore.
What happened to all those races was a Player that craved the ultimate power. I think you all know who'd that be. Herobrine. Or at least that's what he's been called since he changed.
He somehow managed to create the End Portal (let's remember that to craft the eye of ender we need to murder the Endermen and use blaze powder, gained from the Nether; kind of a combination of both) to enter the Aether, possibly accessible only by Aethermen teleportation (unlike the Nether and the obsidian portal, which we can simply craft ourselves). The strongholds probably would be his creation, too. What he attempted to harness must have destroyed the Aether, turning it into the cold, dark End, leaving nothing but shadows, rock and abandoned cities. It would explain the Ender Dragon (a guardian made to destroy any Player that goes through the portal), as well as the Endermen behavior (wandering around, gathering resources to rebuild their lost world and attacking, once they recognized the Player, as the Player equals Destroyer). Herobrine's actions affected all other Realms as well, as the undead and other monsters started to appear in the Overworld. It could also technically explain weird Minecraft physics (the result of merging with the Aether) and wandering farm animals (leftovers from the previous civilizations).
And Herobrine disappeared. We don't know what happened to him, do we? He could have just died, vanished or maybe hid somewhere, that's another open topic.
So yeah, um, I wasted so much time on this >-<
Hope anyone finds it interesting or sth.
ps. I guess similar concepts had already emerged in the past, but why should that stop me from sharing, idk.