What are your thoughts, fellow miners?
Well for one, i'm pretty sure that the ancient civilization had Nether access due to those Nether portals which being the first a player is likely to run across and spawning at the highest elevation probably predate the End and Inactivate portals. Another thing to note is the bastion ruins from the Nether and the pigmen inhabitants, the pigmen seem to have been first created exposing pigs to the nethers environment like how the player can create zombie pigmen by zapping pigs with lighting.
But whether the pigmen where mad or were already inhabitants of the nether doesn't really matter, I think the bastions where created as housing and mining complexs for pigmen slaves so the Ancients could acquire natural resources like netherite and gold from the nether at little expense to themselves, but like most things the operation seems to have collapsed with the ancients.
On the collapse of their civilization we both see tons of zombies wandering around, can find Wither corpses in the form of fossils, and the disc in the deep city has Wither sounds and Warden sounds as well of the sound of a portal opening.
So my theory is that a combination of undead attacks and one or more Withers being set loose in the Overworld caused the ancients to retreat underground and build the stronghold and the End portal, but the End is both really shit and full of hostiles and warships.
Forcing them to leave the strongholds and deactivate the portal. Finally in they build the inactive portal in the deep city since they didn't learn their lesson from the last time, cause the warden to attack them and the skulk infection to take root at the deepest layers of the world.
On the Endermen themselves I think their story is fairly straightforward, their home sucks and they want to invade and teraform other worlds so they don't have to live in such a shitty dimension anymore, as evidence by the Warped forest from the nether.