MASSIVE SPOILER WARNING-This editorial discusses critical plot events in Assassin's Creed II and should not be read if you are going to play through the game.
First of all, let's just say that it's really creepy when Minerva breaks the fourth wall in some sense and looks directly at you when she talks...although you don't notice it the first time. Let's start with the obvious: Minerva could see into the future and know that Desmond would be getting this message in 2012 by visiting Ezio's genetic memory, so Ezio's overall role is just as a relay to Desmond (for the first time noted as extra special compared to the other 16 test subjects). Minerva herself is of a humanoid race that predated human beings on Earth as a highly advanced civilization. Minerva's people--interpreted by humans' later descendents as gods--created human beings in their image as somewhat of a peon class. Through some of your research in obtaining the glyphs, you learn that scientists have discovered a neurotransmitter in the human brain that seems to serve no purpose, but in reality that neurotransmitter is activated by the Apple of Eden, which allows humans to be controlled. You also learn that the Templars (presumably) plant evidence of the "missing link" in human evolution so as to distract people from the Truth that they were created. (The glyph puzzles also basically say that every great historical figure used a Piece of Eden to achieve their success).
Anyway, back to Minerva, she says that a war eventually breaks out between her kind and the humans (more on that in a bit). While both species were consumed by war, a cataclysmic event involving the sun ravaged the Earth (flipped the polar magnetic fields). Despite that Minerva's kind were more advanced, the humans had sheer numbers and were able to survive while only few of Minerva's kind remained. The few remaining and the fact that they had created humans further holds up that this is how humans developed the concept of gods and referred to this species as such. Anyway, as Minerva's kind died out they built vaults (housed in great temples) to relay this message to the future so as to avoid humans from the same fate when it happened again. After the very end where you can here the Assassins talking to each other in the truck, you learn the bit about the cataclysmic solar event. Desmond's story also takes place in 2012, a year that is famously associated with cataclysmic disasters and polar reversal is one of the leading theories.
So that's where Assassin's Creed III will be going, but what about the rest of this crazy backstory? Well The Truth video from the glyphs is a memory of Subject 16's, mean that he is a direct descended of either Adam and/or Eve from the video (by the way, the Adam/Eve names justify the Biblical story of human creation, especially the Forbidden Fruit). Since Adam and Even were basically the first Assassins, that means that all Assassins are of their descent. What is likely is that Adam and Eve may be a hybrid of Minerva's species and our own, or that one of them helped a human escape and steal the fruit. In any case, their descendents--the Assassins line--are separated here from the rest of the human genome. Anyway, Adam and Eve steal the Apple from Eden in this sequence and likely start the human rebellion that Minerva spoke of. The Templars must be a sect that has knowledge of the Apple and the Pieces of Eden and want to use that power to indoctrinate the world (perhaps related to the Assassins line but went bad). Minerva does say that Desmond will have to "fight against the Cross" and the Templar's symbol is a cross. The rest of the world has forgotten all about the Pieces, referring to them only in mythical stories (such as Adam and Eve and the Forbidden Fruit).
So there you have it, what are your theories? This is crazier than even National Treasure or a Dan Brown novel. One of the few examples of incredible video game narrative.
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