Okay, so suppose the Ancient Kingdom was this awesome place where everybody was happy…sort of like a One Piece Garden of Eden. The Kingdom was further divided into three sub-countries. One country could use their bodies to perform amazing feats (Paramecia), another could transform into animals (Zoan), and the third could harness the powers of nature itself (Logia). The ruler of this Kingdom was fair and just, and his royal bloodline was marked by the initial D. This man is Luffy's ancestor.
Many of the kingdom's citizens could not use any of the Paramecia, Zoan, or Logia powers, and were therefore immensely jealous. They formed their own country, which the just king of D. recognized. This small country, however, began constructing a large weapon (Poseidon). Upon hearing word of this, a shipwright began constructing a counter-offensive measure (Pluton) should the small country ever complete Poseidon.
Scientists from the ever-growing split-off country began to research ways to absorb the powers granted to the country of D. at birth. After painstaking research and kidnapping test subjects, they were finally able to produce an ability of their own in the form of a fruit: the Yami-Yami no Mi. It granted the person who ate it the ability to control darkness, although water made it and the user totally useless. They were able to use this power to steal the abilities of others, one by one. They culminated their research and fired a darkness shot from Poseidon which impacted the very center of the D. country. As its toxins spread, the citizens of D. each lost their abilities. With every ability lost, the ruler of the rebel country grew ever stronger, until he had every ability imaginable. When Pluton was finally completed and used to destroy Poseidon, it was already too late.
The country's citizens turned to their king for help. The king promised to save the country (which was his treasure) and its citizens (who were his friends/nakama). He made but one mistake: he went alone. Had he gone with his friends, he would have succeeded.
The rebel leader had the same weakness as Blackbeard: he was too cocky. Ancientbeard (as I've decided to call him) had all the power in the world, and nothing could ever stop him! Zehahaha!
Luffy's ancestor looked Ancientbeard in the eye, said "I'm gonna kick your ass!" and used his Royal Haki to subdue him. Luffy's ancestor then used the most epic Haki-infused punch ever on Ancientbeard, and all of the abilities he had collected turned into fruits and were scattered across the globe. But the last attack made Luffy's ancestor collapse on the ground and die with a smile on his face.
All was not well, though. Ancientbeard had used the power of the Yomi Yomi no Mi just before he lost it to revive himself as a spirit, and wandered the world until, centuries later, he found the perfect vessel: Marshall D. Teach. Teach had the will of D., but also had just enough greed and spite in him that he could handle Ancientbeard's evil. That's why Teach has "two lives" and an "abnormal body," because he is fused with Ancientbeard.
Anyway, I'm going to keep going with my story since I got way too into it to stop here.
Though Ancientbeard had been defeated, the war was still ongoing. Ancientbeard's followers and their advanced technology conquered the D. country, who had been relying on their abilities for so long. Most of the king's descendents were either killed or enslaved, but some survived. The citizens themselves were mostly enslaved, though things began to mellow out after a time. A number of scientists who had originally supported Ancientbeard now disagreed with the way things were going, and so fled to the Moon the escape death or enslavement.
Eventually, of course, someone found one of the ability fruits. The elders were shocked and immediately seized the guy who found it, and made him eat it. After seeing the results, they declared his power the work of the Sea Devil, proving it by throwing the poor guy into the ocean and watching him sink. Thus the fruits came to be known as Devil Fruits and, though they were at first forbidden, they eventually became the center of much scientific research.
Throughout all this, reports of the mysterious stone tablets called Poneglyphs came to the elders. The Poneglyphs told of Ancientbeard's rise to power and tyranny, and also of the valor of Luffy's ancestor, the king. The elders wanted to destroy these Poneglyphs but were unable to. Finally, they decided to simply execute anyone who tried to research the Poneglyphs and that put an end to that...until Ohara.
Anyway, as you can at this point probably tell, Ancientbeard's rebel country became the World Government, formed completely out of spite, contempt, and envy. As the generations passed, some of the True History was forgotten, while bits of it remained engraved in the hearts of men. The only truly permanent thing was the continually carried-on Will of D. and Ancientbeard's greed.
So yeah, that is my theory. Thing. Does it sound too fanfic-ish? I just kind of thought of it as I went along and it seemed to sort of work.
And as I go back and read through my wall of text, I'm now expecting a bunch of "tl;dr" responses.