This is a theory I have about many of the major plot points in One Piece. Many of these are similar to other theories floating around, but I'll try to organize this a bit better. But this is a lot of information, so unless you read all of it, don't comment.
The first point I want to make Is about the Ancient Kingdom which existed in the Void Century.
! From what Clover said, we know the ancient kingdom had enemies and left behind Poneglyphs to spread a message. They were also a Great Civilization and when Clover tried to say the name of the Ancient Kingdom he was killed.
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The next thing I want to do is jump to Enel's cover story and also explain the Ancient Kingdom and 20 Kings.
! On the moon, Enel discovered an ancient subterranean city called Birka, which has a picture on a wall showing a Skypiean, a Birkan, and a Shandian all working towards a common goal.
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! Now this where the theory starts to pick up, I think it's safe to assume that the winged races all originate on the moon and created wonderful technology(Dials, Robots etc.). But due to a shortage of resources on the moon they left for "Earth". They initially settled in the Cloud Sea, but then decided to go down to the surface where the humans and other races lived. The Sky People were welcomed by humans, and they both shared culture and technology, thus the Sky People and Humans established the Ancient Kingdom. The name of this Kingdom was "Raftel" where the Devil Fruits were created. The World Government is trying so hard to keep the name a secret.
! The next part of my theory deals with the "20 Kings" that formed the World Government. I believe that the 20 Kings were also "aliens" who lived on the other side of the moon and that they have the ability to shape-shift. Seeing how Oda uses a lot of influences from pop culture I think the 20 Kings and their descendants the "Celestial Dragons" or "Tenryubito" are really shape-shifting Grey Aliens. Now I know this sounds crazy but it makes sense. The world nobles seem to have a "space" theme with their astronaut suits and heavenly name, and also the fact that they don't consider themselves human.
! Its been speculated that Oda got the design of the Celestial Dragons from the movie "The Adventures Of Baron Manchausen" in which the Kings Of The Moon heavily resemble the Celestials.
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! The 20 kings settled on earth as well and gained human followers just like the winged people, but the 20 kings could never keep up with the ancient kingdom and started to lose followers.
Now the theory moves onto the Void Century.
! I think we all assume that the Void Century was the war between the ancients and the 20 kings, which is made obvious by Clover. The war must have been deadly for the ancient kingdom, and they feared the 20 kings enough to create the Ancient Weapons(I'll elaborate on those later) and to put the information of their culture and history throughout the world on "Poneglyphs". The 20 Kings started a genocide against the Winged People. Somehow the 20 Kings managed to defeat the Ancient Kingdom and with the Ancient Weapon "Uranus" which has the ability to cause major earthquakes and move tectonic plates, created the "Red Line" to signify their domination over the World, to make Holy Land and to separate the 4 Seas, thus creating the "Grandline". The Shandians were on Jaya because their ancestors fled there to escape the war. The rest of the winged peoples went back to Skypiea
! This is where the theory gets really wacky but it has some basis. I think that Jewelry Bonney is a survivor of the Void Century. How can this be you ask? I'll explain. We've seen that Jewelry Bonney has a Paramecia-Type Devil Fruit that allows her to change peoples' ages from young to old and old to young. Also, in an SBS, Oda gave the ages of all the Supernova's and said Bonny is "24 (Estimate)" which sounds awfully suspicious to me(or anyone). This might not be true but I think that The Gorosei or "Five Elder Stars" are 5 of the Kings that overthrew the Ancient Kingdom that use Jewelry Bonney to keep themselves young(old rather, but you get the point). This explains why the government was so concerned about Jewelry Bonney escaping them.
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! I also think Jewelry Bonny has the child of Portgas D. Ace, which would explain why she was so upset during
his execution.
Now the big one, the Will Of D.
! To start off, when the Winged People established The Ancient Kingdom, I think that they had offspring with humans. This small group of people who had both the "Angel" genes and "Human" genes are the carriers of D. The D. represents the half moon as in "These people have half the bloodline of the moon". Looking at the cover of volume 27 makes me believe this even more, we see Luffy with wings, winking as if he is hinting at something.
! Those who carried the genes of both races had to place the burden on their descendants to overthrow the World Government. Joy Boy was probably one of the "D's"(Ancestor Of Luffy?) that brought Noah to the ocean floor and knew that one day the Fishfolk and Merfolk would have to come to surface to aid in the destruction of the World Government.
! My theory about the ship "Noah" is that it will be used to carry the Fishfolk and Merfolk to surface. Look how big it is! Roughly the size of Fishman Island, so it can definitely carry all of them to the surface.
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! The purpose of Shirahoshi(Poseidon) is that she will call on the Sea Kings(The only ones capable of carrying Noah) to bring it up to the surface. They may also aid in the final battle against the World Government.
! Moving onto Pluton, one of the Ancient Weapons, we know that it was constructed during the Void Century which goes with my theory that the ancient weapons were create to fight the 20 Kings. I think Franky will build it for the final battle.
! The last mentioned weapon is "Uranus" which, like I said before will be used to destroy the Red Line. Uranus will be on Raftel alongside the Rio Poneglyph, which will have the last piece of true history. Uranus will make an earthquake that will cause the Red Line to collapse, thus causing The Four Blues, The Grandline, and The Calm Belts to come together uniting the world into "One Piece" and creating The "All Blue."(Sanji's Dream) This will all be possible with the "Will Of D."