Whenever someone mentions Villagers, you will likely think of people who rip you off at trading, extremely passive and vulnerable, somewhat stupid. I don't think so, my question is: "Did we underestimate them too much?". I mean, they are human, the same as players, so why do we tread them like that... Because, we only observe their outlook, what about things they're keeping in the village that reveals their true past?

"What? They're keeping stuffs in the village?" Yes, they do. The answer is simple, it's where you always go to to get loots when confronted a village, blacksmiths. In many cases, there is a chance for obsidians to be generated; let me tell you: obsidians are the clue which lead to my theory: The Villagers went through dimensions and are the one who built mineshafts.
Why obsidians are the clue? Well, why do they need them... Of course for the Enchanting Table but do you know the amount of obsidians generated will be from 3-7 (while Enchanting Table only needs 4) So to conclude, I think that the obsidians in the chest were the left over part from making the Nether Portal. Another evidence is that in the Nether Fortresses, there are chests that contain tools of the Villagers such as Saddles, Horse Armor, etc. Thus, Villagers like agriculture, so no wonder why there are mushrooms (Nether Wart you call it) planted in the fortresses. Eventually, they have to abandoned it since the mobs are too hostile.

When you think things couldn't get more "cray cray" (ok I shouldn't use that), I meant crazy XD , it did. From the Overworld, in the village's farms, they plant beetroots, right? This is also a major clue to my theory. As you know, you can get beetroot seeds from End Cities. My opinion is, the Villagers did also go to The End! Crazy, right? Same as the Nether, End Cities have chests that contain familiar stuffs from the Villagers like armors, tools,... If you didn't read my last theory, I said that before you could go through the End Cities without defeating the Ender Dragon, the Villagers came there that way. Unlike the players, they are nice, that's why Endermen don't attack them and let them stayed. After that, the Endermen created the "between land" and the dragon (because they want to stop the players from destroying their land), the Villagers realized that they have to go back, which they left the chests fill with MLG stuffs in there.

Nevertheless, we also found beetroots in mine shafts, which means the Villagers once worked under there and they kept the seeds in case they ran out of food.

That's it for today guys, hope you enjoy my theory! :D