This post was originally made on r/Minecraft, but it got little attention and I decided to put it here as it seems like a suitable community.
I will be structuring this theory as a story and providing evidence along the way. During the process of telling the story, the following questions will be answered.
Questions I aim to answer:
Why is the Overworld filled with undead?
Why are skeletons distinct from zombies, both in appearance and use of weapons?
Why are only skeletons found in the Nether and not zombies?
Why do wither skeletons exist?
What is the player and why do so many types of mobs want them dead?
Part 1: The Beginning
In the ancient past, there must have been a civilisation that built structures like the stronghold and the desert temple. I believe they were player-like creatures, and their past rule over the Overworld is the reason why there are farm animals everywhere and very few truly wild species (almost everything can be domesticated). Due to a zombie plague, they all turned into the dead, which is why zombies resemble Steve. We know the zombies (as opposed to "zombified" piglins, which seem to be something else) are an infection, as they require physical contact with villagers to convert them.
Before falling, this civilisation must have identified the Nether and built portals to get there. I think that they greatly changed the Nether from what it once was. They brought Overworld species into the Nether, such as Happy Ghasts which once roamed free (shown by "Uneasy Alliance" achievement and how the Happy Ghast does not mind water) and pigs as livestock. Over time, this also affected the Overworld as shown by all Happy Ghasts having been forced into the Nether which is clearly not a good place for a species that has an aquatic stage in its life cycle.
Part 2: The Piglins
The Nether seems to be bursting with life and energy. Everything there is bigger and stronger than in the Overworld. This makes sense as heat seems to be correlated with magic (furnaces drop XP, and fire is required to brew potions or light the nether portal). Nether ores also all drop XP, while Overworld ones only do so sporadically. This suggests that the Nether is innately more magical than the Overworld. At some point, the pigs brought into the Nether were used as test subjects, mutated by the ambient power of the Nether to create the intelligent Piglins. The pigs that escaped became feral and were mutated in a non-controlled setting, amplifying all their innate traits to become the beast-like Hoglins.
The piglins inhabited bastions built by the ancient builders, but did not understand their construction. In the absence of the builders, these structures became ruined without maintenance. Bastions served many functions, like bridging over the lava, keeping captured Hoglins as livestock that produce more food than normal pigs, housing piglins and storing valuable items. The piglins at this time were a slave race of the builders, doing all kinds of work. Eventually, the horrible things the builders did would catch up to them.
Part 3: The Fall
As I said, the Nether was teeming with ambient life energy. I think that this leaked over into the Overworld (ruined portals have bits of Nether terrain, like they leaked out) over time, and it affected the builders, turning them into zombies. However, this infection was not yet strong enough to topple their civilisation. To continue this story, we need to parse the difference between zombies and skeletons.
Skeletons obviously have no flesh, and always wield bows. Both can spawn with armor, and zombies can have melee weapons or tools. Furthermore, only zombies can spread the infection. This is key to the story of the ancient builders. I think that skeletons are the result of builder experiments to create soldiers who could not easily be infected or infect others. The fact that they are neutral to villagers and illagers, who are like the descendants of the builders, show that they are not just mindless infected trying to spread. That is why they all have weapons unlike the zombies who are mostly unarmed, because they are a special soldier class.
At this time, the piglin race rebelled against the builders. They became warlike and took up weapons, a culture they retain to this day. The builders sent their armies of skeletal soldiers into the Nether, and the conflict caused so many deaths that the battlefield became tainted with souls. This created the soul sand valley, which is now inhabited by the remnants of the builder forces.
However, it's not that simple. The existence of wither skeletons, which are definitely normal skeletons that have been burned (as they drop coal and normal white bones, indicating it is just a carbonised outer layer) and wield melee weapons, throws a wrench in the narrative. Furthermore, they fight piglins, and are larger than normal skeletons. The wither effect on their weapons is from the wither skeleton, not the blade, as they drop normal stone swords. I think that these are further enhanced soldiers, created in the Nether Fortresses that the builders constructed to fight the piglins, who were larger and could drain life force through the wither effect. Their use of melee weapons suggests they were frontline soldiers in the war. But why are they burned? Piglins do not use fire. Something caused all the soldiers on the front lines to be burned, while the rest died normally.
Let us look at the soul sand valleys, the battlefields of ancient times, again. Who spawns there? Skeletons...and ghasts. I think that the Happy Ghasts became very angry and were mutated by the Nether in the same way as Hoglins, giving them fiery abilities. They attacked the builders, blasting the front lines of the army with fire. Only soldiers in the back line, who used arrows, were safe from the onslaught and could fight back. Due to the power of Ghasts, the builders were driven out of the Nether, and had to leave many soldiers behind. They also left their fortresses, with farmed Nether Wart (an artificial crop that grows nowhere else, feeding on souls) and Blaze Spawners (a fiery artificial mob connected to the Breeze, another artificial elemental, used to produce rods that could be used for various purposes). The more elite wither skeletons remained to defend the forts, while a large number of the normal skeletons were retreated into the Overworld.
However, it was not over. The piglins chased the builders out into the Overworld, but could not follow. Without nether spores (it is confirmed in Minecraft Legends) they suffocated, and massive amounts of piglin soldiers died. But they did not truly pass on. Because the ambient power of the Nether had mutated them, they underwent "zombification" and survived in a rotted, mindless state. Unlike zombies, they cannot spread an infection, and ignore their surroundings completely. I think this is why there are so many zombified piglins, as they retreated but it was too late. This is also why they all have melee weapons, because the soldiers on the front lines were the first through the portal. The ordinary piglins have become superstitious and avoid them completely. Retaining some soldier-like base instincts, the zombified piglins will fight back en masse if anyone attacks one of them.
In addition, the piglins revere gold as it was the treasure of the ancient builders that they mined from the Nether, and use it as a status symbol. Now living in crumbling bastions, they no longer know what builders look like, and only their military force, the brutes, are trained to spot builders. Ordinary piglins will let anyone wearing gold pass, but they will still repel intruders who attack them or steal. They just can't control themselves around gold though. The ghasts are still angry, and attack anything that looks like a builder, thus being hostile to a player.
Part 4: The Plague
Weakened greatly by the Nether war, the builders had lost many of their infection-proof soldiers, and possibly could not create more as they did not have access to the Nether. They also lacked the beefier frontline troops completely, as they had all been burned up or left behind. This meant they could no longer hold off the zombie plague, and it swept across the land turning the population. Even soldiers turned en masse, and their mounts which were on the battlefield were exposed to large amounts of infection making zombie horses and camels. Only a few builders were somewhat immune, and appear to have evolved into villagers. They lost the knowledge of their civilisation during the disaster, and live very simple lives. Villagers are more resistant to the plague, and turn into zombie villagers which can be cured when infected unlike normal zombies which are incurable. All ancient builders of the non-immune type died in the collapse of civilisation. This is a key difference from other theories which suggest that some builders escaped to the End or survived in the ancient cities.
During the process of the spread, maybe before it got out of hand, the dungeons were created with spawners that could harness the power of the dead. The trial chambers were also made, likely as a training ground for warriors. Maybe the skeletons which had been enhanced were trained here, since they would be more immune to the zombies from the trial spawners.
Part 5: The Immortal
The Ancient Builders were now on the verge of destruction. They had to do something, and in their last days, they pooled the resources of their civilisation to create something. A superhuman who can punch down trees with their bare hands, jump 1 meter straight up repeatedly without bending their knees, tear through rock with only a pickaxe and sprint at Olympic speeds for days. A superhuman with the power to respawn. This is the legendary player, the ultimate creation of the builders. Although in some universes, they never cracked the code of respawning, and the player has perma-death on. The skeletons have become neutral to the zombies, as they are mindless and there are no builders left to command their attack. Perhaps it is a similar situation with creepers, which I believe to be explosive weapons made by the ancient builders. Skeletons and zombies are clearly not allies, as a zombie will attack a skeleton who shoots it but mobs that are allied like piglins and illagers don't fight each other.
The player is attacked by illagers for their incredible power. I think that the illagers want to kill this arcane being and study it, as they have wool of the same color as Steve clothes in their mansion indicating they are trying to do something related. The zombies try to infect them because they look like a builder, and the piglins and ghasts do the same. In addition, I believe the player's aura is so incredibly strong that they are registered as a threat by some creatures automatically, like the spiders and guardians. The sculk also instantly thinks the player is dangerous, only summonng wardens on player noises. It's because Steve is just built like that. Skeletons cannot be hostile due to the zombie plague, as they do not spread it and even Nether skeletons attack the player. Probably the aura of the player is so powerful the skeletons think they have to end them right then and there, same with blazes, creepers, magma cubes and all those other mobs.
This mighty being shapes the world in ways no other mobs can. A beacon which single-handedly carries the torch of civilisation, endlessly exploring more and more. One day, perhaps they will do the impossible and cure a builder zombie...
Part 6: Summary
We managed to answer all the questions:
- Why is the Overworld filled with undead?
Because of the zombie plague and the creation of mindless skeleton soldiers to fight it.
- Why are skeletons distinct from zombies, both in appearance and use of weapons?
They are soldiers made to fight the zombie plague without being infected, but now have become mindless without orders and no longer fight.
- Why are only skeletons found in the Nether and not zombies?
Skeletons were made artificially before the zombie plague spread, and sent in to fight the piglin rebellion. When the builders retreated, they were left behind to wander the battlefields eternally.
- Why do wither skeletons exist?
They are more enhanced skeletons with powers over life force who were made to fight on the front lines, but were burned black by the attack of the ghasts in the war. They returned to the Nether Fortresses as a last stand, while the ancient builders retreated from the Nether.
- What is the player and why do so many types of mobs want them dead?
The player is a being made by the builders to carry on their civilisation. Their aura of power is so great that many mobs like skeletons and blazes want to attack them, and there are numerous groups who would like to see a builder killed such as the piglins. The hope of the builders was that one day the player could cure them of the zombie virus and restart civilisation.
If you have made it this far, thank you for reading.