Pieces of Eden, including the apple (one of heaps of apples) are left over pieces of technology from a civilisation that existed in Earth before humans did... and are hinted to have created humans. They were known as the First Civilisation.
Humans rebelled against them Stargate style and a war broke out, because Adam and Eve were the leaders of the human side and they had first civilisation dna as they were created as hybrids and as such had the eagle vision thing... which is a kind of jedi mind trick used to determine ally from enemy by a kind of telepathy.
So Adam and Eve were the first assassins. After the First Civilisation were wiped out by a massive solar flair, they created the assassin's creed and the assassin's and their origins got lost over time.
Eventually the tech left over from the first civilisation is rediscovered, and both assassin's (who seek to protect it from misuse) and the Knights Templar (who want it for world conquest) fight over it.
The apples of eden are specifically good at mind control as they were built to ensure humans would obey the first civilisation.
So the templars and assassins have been secretly going at each other behind the scenes of history, over these powerful ancient tech, with the templars eventually becoming a massive conglomerate called Abstergo.
One of Callum's ancestors was an assassin and using a device Abstergo invented, called an Animus, they want to plum through the memories of Callum's ancestor (this is what an Animus does, allows you tp relive genetic memories of your ancestors still present in your dna... like the Matrix) to figure out what he did with it.
It's... complicated. And we aren't even in Victorian London and the quest for magic healing cloak yet.
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