Well, I just had an idea for what the true story is behind Minecraft. If you hate this, I don't want to hear it.
So, the Minecraft world was originally a regular, blocky enviornment with cities, villages, and societies. It was a blocky version of Earth. So later on, some scientists were testing a chemical on our protagonist Steve. The chemical was supposed to test human strength, knowledge, and speed. Steve was made a human like no other, allowing him to never die, cut down trees with his hand, giving him knowledge of potionery,craftsman skills, and other skills shown in crafting. However, the same scientists accidentally caused a leak into the ground, which made zombies, skeletons, mutated spiders and mutant explosive creatures (creepers). They quickly rampaged through the land, killing everyone, except Steve and some other humans. The current slimes were also a failed experiment who were abandoned in the wild. The other humans were infected and became the current derpy villagers. Some went insane and became the witches. Steve was trapped in an apocalypse. The only option was to survive. He later on discovered the old temples, which leads his adventures through the nether and the end, which were considered a legend. Steve remained to live his life, to freely roam the world, to build, destroy, and to conquer. It's not the best, but it's what I think of Minecraft survival as.
I presume that means the Wither and Ender-Dragon are ancient demons (?) that have heard of Steve's legends and are prepared to face him?
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My avatar- Madison Gotha, Queen of Gotha. Madison is extremely powerful, mastering magic, many weapons, and several other skills, such as forging and thievery. She's a dimensional traveler, a dimensional ambassador, and a tamer of many monsters. She has two children, Lyna and Dosey, twin baby girls. 25 Years old, and a Lofty Peakian/Zenithian Mix. AKA, Not human/elf.
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I think another way the mobs in Minecraft came are from the portals such as the End Portals, Nether Portals, and that the creation of the strongholds caused the mobs to come out and wreck havoc, a bit like Half-Life's resonance cascade at Black Mesa.