Alright, so as we probably all know, there is a more complex story behind Assassin's Creed than is shown in the games. I have a theory that is based on the 'Truth' video, the entirety of both games and all the hints within. I think this is a sure-shot theory and to me it makes perfect sense, so let's start. Voila my theory, in story form:

Once upon a time, on a planet named Earth, there was a civilization named Eden. Eden was a very powerful civilization, so they decided to use their powers to create something... they would be called, humans. The first two humans to be created were named Adam and Eve. They're job was to continue the human race, to give Eden more slaves to work for them. But one day, Adam and Eve stole the mighty Apple of Eden, one of the Pieces of Eden, used to keep humans in line. Why? Simply because they thought it wrong to be slaves of Eden, and that they had the wrong idea to keep peace. They ran and they ran, climbing walls, performing many acrobatics that today seem impossible. Then, they were captured, with the Apple of Eden in their hands. They fought and they fought, but they could not defeat Eden, so they simply escaped. And they founded a plan. A plan that will ultimately win them victory. Use the Pieces of Eden on the sun, to destroy Eden.

They would capture the other Pieces, and use they're magical abilities on the sun to create a super-flare, which would kill anything on Earth. But what about themselves? They would die too! So they created temples. Not just any temples but powerful temples that, when used properly, would save them from the super flare. And so they created the temples, created the super-flare and destroyed Eden along with all they're creations, other than the Pieces of Eden, of course. This would eventually lead to Eden becoming simple legends, myths, as the new human civilization grows stronger and more corrupt. Built just as they were meant to be: to survive. Minerva, Juno, Jupiter, among other names, were remembered. Remembered as gods, which was untrue, but as mentioned above, they became legends and myths. Roman legends and myths(the names Minerva mentioned at the end of ACII were all the names of Roman gods).

As man kind grew stronger and larger, different beliefs were born. But two main beliefs are in the Assassin's Creed story. Peace through the Pieces of Eden, and natural peace. The Templars, who followed the same beliefs as Eden, peace through the Pieces of Eden, would try to find all the Pieces of Eden and use them to essentially brain-wash mankind into peace, giving them power over all others, save the few that could resist the power of Eden, who they would have to kill. The Assassin's order, who believe in natural peace, would try to stop the Templars from achieving their goal, ultimately resulting in mankind taking it's own coarse for peace.

For years these two groups fought. We saw this first from the perspective of Al-Tair, one of the Assassins who single-handedly destroyed the Templars of his time, as ordered by his master, Al-Mualim, who he also killed, for he turned out to be a Templar himself. After killing Al-Mualim, Al-Tair wanted to destroy the Piece of Eden, but something was stopping him. Afterwards, he brought the Apple of Eden to Cyprus, which leaded to our second character, Ezio. Ezio's family was unjustly killed by the Templars and so he sought revenge, and that he got. But it turned into more, the leader of the Templars obtained the Apple of Eden from Cyprus, and the Staff of Eden by becoming Pope, and attempted to use these to open the vault, containing secrets only the prophet can unlock. Of course the Spaniard thought he was the Prophet, but really, the Prophet was Ezio, who defeated the Spaniard and unlocked the secrets of the Vault. He was confused, for he was but a messenger for Desmond, our not-so-distant future character. Poor Ezio, his entire life leading up to said moment.

Of course the secrets in the Vault depicted what lead to this story, the temples, Eden, the Roman gods, etc. But there was one shocking bit of news from Minerva, a now dead last survivor of Eden. Earth was due for round two. This meant that the Assassin's enemies, the Templars, now Abstergo, were not the largest threat. The sun, was the largest threat. Minerva for-told that there would be another super-flare, destroying Earth once again. Of course, unless someone can find the temples and use them to guard themselves, and reproduce mankind a second time. And I think we know who that will be.