Like many others before me, I will now deal with the obfuscation of facetious assumptions and theories. I'm interested since a long time into the metaphysical aspects of the Assassin's Creed saga and all the secrets that surround it. What I mean is I think the series has a message of great importance to our modern era. The saga takes us to the heart of various moments in history and we discover in each of these time periods that mankind hasn't changed at all. The conflict between Assassins and Templars is only a pretext to represent it. Furthermore, these two orders are much more alike than they differ from each other. They share the same ideology and their ultimate goal is to ensure peace (in everything), although the means they use are divergent: the Assassins, considered as fanatics, follow a creed to ensure the free will by killing all those who go against their beliefs and the Templars, in the meanwhile, desire to get the ultimate control by any costs to avoid chaos. They've been at war for thousands of years while they initially wanted to avoid it. I think the trauma of the war between humans and the First Civilization and the worldwide catastrophe that followed is the source of their conflict.
The important thing is to understand that the saga has a deeper meaning rather than just reviewing the history from a new angle. Everything boils down to one thing: the Assassin insignia. Many people associate it with the symbol of Freemasonry. But this is wrong. During my research, I've come to associate the Assassins insignia to the Alpha-Omega (Α,ω), which is symbolizing the eternity of Jesus Christ. As we all know, the saga also features various religious and mythological elements (in particular through the First Civilization). Alpha and Omega are also the first and last letters of the Greek alphabet. They symbolize the beginning of everything and the end of the world. Technically, when you think about it, they symbolize the cycle of history repeating itself without end: the creation of life to its annihilation, constantly (the First Civilization created mankind, then they disappear and humans emancipate themselves and spread across the Earth until their eminent demise). Alpha and Omega is mostly present with the Chi Rho (P marked with an X). If you are observant, this symbol was repeated many times on the walls within the Vatican Vault. It's true that at first sight Alpha and Omega don't look like quite the insignia. But if the honrizontal line is removed from the letter Alpha and we place a lowercase Omega underneath, we notice then it looks much more like the original Assassin insignia, except the fact it has been slightly changed and artistically improved.
So it all boils down to this: the history of life is that of war, a cycle of creation to its inescapable destruction, and everything repeats itself again and again. And in this current cycle, there are the Assassins and Templars trying to do their best to restore order and peace since the Precursors' extinction.