I think that skeletons are different from zombies, they often get put grouped together and just explained as "Zombie Plague" or simply undead. While the zombie virus theory might be true for the zombies, I think the skeletons actually are the dead builders that didnt become zombified. After they die, their souls are trapped in the soulsand in the Soulsand Valley in the Nether (Supported by the fact that they spawn there naturally as the only mob aside from the ghast, which i'll come to later). There, they are tortured (as you can see from the screaming faces in the soul sand) until they are in such pain that they are under the command of the wither or just evil. Their souls reemerge as skeletons. But there is a plothole: How is the body of the skeletons formed? This is fairly simple: The fossils of the old creatures contain bone blocks, from which the bones of the skeleton come from.

Hypothesis of the creation of Steve and Alex

it starts when this race of master builders became trapped in the end. A young man named Steve and a young woman named Alex got left behind, they died. Hundreds to Thousands of years later, an illager came and resurrected the corpse. Likely an evoker as they drop totems of undying and spawn the vex which are ghosts that he summons to do his bidding. Evokers are likely obsessed with cheating death. He, after figuring out a way to cure zombies, wants to use it to make an army to do his bidding and tries it on you as a zombie. You come back and conscious of your past life, you kill the evoker with your bare hands and go on your way, then you start your journey as you remember the wither, stronghold and netherworld, the ocean monuments. Your journey begins.

Theory: rebirth of the master builder race.

evidence: Alex and Steve are survivors to repopulate; Villagers are rediscovering their crafting abilities: crafting tables, grindstones, armoring, fletching, clericalism; Illager enemies which force the villagers to innovate to survive; the end freed: the theory suggests that the endermen “evolved” from this race of master builders, now that they can go back, they can one day turn back into this once great race of master builders; Steve and Alex demonstrating their crafting abilities infront of villagers: imagine going about your day and a stranger walks into town with full enchanted armor, night falls, iron golem is distracted, zombie is knocking down your door, then the player dashes through the zombie with a speed II effect, you and your kids become inspired to do more, suddenly a creeper comes and gets close to the player, a cat appears net to the player and scares them off, a skeleton comes, the player takes his shield and deflects the arrow back to him, the villagers see you as unstoppable, next day player comes, illagers raid the village, the player defeats the evokers, the ravengers, the pillagers, the vindicator and the witches, the raid is over, out of his pocket, the player grabs a potion and heals, is there nothing this man can’t do?, weeks later you see him crafting, he is making a new sword, you ask him how you do that, he tells you and suddenly everyone is crafting weeks later: the theory suggests that the villagers once split from this race of master builders and survived by forgetting to craft but now enemies rose forcing you to be innovative once more as matpat’s theory suggests.

Lore question: where do zombies and come from? What caused their undeadness Based off of matpats theory of master builder race.

Theory: the warden and the skulks are the ones who got left behind and evolved to live underground. And the warden is there to protect the skulks

evidence: The warden’s human like structure including a chest cavity and a heart. The warden is called a warden, wardens are referred to as the director of a prison.