So, I hope that all of you who are reading this are aware of the Game Theory Video series that is currently in production addressing the lore of Minecraft. For those of you who have not viewed it, it basically goes to claim that the original builders were masters of civilizations, building, and exploration. Upon going into the Nether, they discovered that when someone died, the ground sucked their soul out, thus creating Soul Sand. All that was left was a charred skeleton. So these geniuses tried combining the bones of a Wither Skeleton with Soul Sand in an attempt to bring the soul back into the body and resurrect the diseased.
And thus, the Wither happened. Here was this beast that destroyed pretty much everything it touched. Places in the Overworld were devastated, the only exceptions being those deep underground, in the ocean, or secluded in deserts. With the laws of nature corrupted, when the Wither made a kill, the bodies of the ancient builders became undead, and continue to crawl out of the ground upon nightfall to mindlessly haunt the lands. This explains why zombies and skeletons and other undead being resemble your character.
The survivors fled underground and created the stronghold. Game Theory suggested that it was called the stronghold because it was indeed a shelter to defend the survivors. Now more familiar with magic, those builders devised a plan to create a portal to take them to another dimension where the Wither could no longer terrorize them.