Origins are sometimes hard to figure out, but what of the beginning of the end?
We all know about The End. Its a plane of nothingness inhabited only by Endermen and the Ender Dragon. But what if I told you that The End is the Overworld and the Nether fused together? Listen to this and maybe you might just rethink your outlook on Minecraft.
We go around in the Overworld building with nearly infinite materials at our disposal. We travel through a portal to the Nether in order to obtain materials that cannot be found within our realm. Now say this. The portal acts as a two way door for any creature. Let us put into a hypothetical situation that the portal started to get bigger and with it both realms were being forcibly merged. Sounds ludicrous, but in all actuality its not. The two realms slowly begin to combine, introducing entirely different species who act aggressively towards each other. Soon, the realms begin to get destroyed with both worlds mobs fighting for survival. Eventual the two separate worlds collapse onto each other with most of life being wiped out save for a species that avoided the conflict (villagers?).
With no resources to cultivate, nor the appropriate environment to sustain their old way of life, the species soon begins to adapt and evolve. This evolution leads to the creation of the Endermen, along with the introduction of yet another species of mob that survived and adapted in which they would become the Ender Dragon. Of course the Ender dragon has evolved to be Asexual and can reproduce by itself in order to keep it species alive. The Endermen however still hold parts of their old self along with the desire to rebuild. In order to do so, they start sending themselves back in time in order to gather materials to rebuild their world. However their form of rebuilding is placing blocks in random locations in hopes that when the future arrives of the two realms coming together, there will be more blocks that survive the merge and more land in The End.
To summarize it up, the Overworld and the Nether will eventually come together and be destroyed in the process, The Endermen will be created and travel back in time to place blocks in locations for the hope of creating more land, all the while we deal with the inevitability of watching all of creation being doomed to repeat its own destruction. The Endermen suffer from possible OCD and Schizophrenia and have mentally deteriorated to the point of not recognizing anything. Their obsession of saving their new world drives them to act out at anything that gets in their way or even looks at them funny.