Eve, The Revolution and The Cycle of Sages
This may seem too farfetched or a bit nonsensical since no concrete information is mentioned about this matter and I doubt we’ll even go this far within the games, but I hope we do, especially with how the whole Eve story never really got a resolution and it keeps disappearing for a while and reappearing again, once mentioned by Clay, later in AC:Liberation via the Disk and now there’s this Lady Eve in AC:U Dead Kings, who was supposed to get the Apple (or whatever this smaller mini-Apple is called).
I think since Eve could acquire the Apple in the first place circa. 75k BC, led the revolution and bring down the First Civ. and since Clay got in touch with Juno and he also mentioned something about meeting Eve, and in the ending of Dead Kings, the Piece of Eden was to be delivered to Lady Eve, as I mentioned earlier. So what are we looking at here? I know that Eve is a common name and it could be just a coincidence, but what if we’re looking at another Sage here? Here’s why I think that:
1. There’s the original Eve, there’s an Eve that Clay wanted us to meet, and there’s lady Eve.
2. Eve led the revolution before against the First Civ.
3. Minerva knew what Desmond will choose (ACIII ending).
4. According to Minerva, surviving First Civ. members worked with the humans to rekindle the spark of civilization.
5. First Civ. technology was still functional after Toba Catastrophe.
So here’s what I think happened: Juno was a benign First Civ. member, one of those who didn’t wanna harm or enslave humans. Humans revolted and murdered Juno’s father. Juno became hateful of all humans. Juno started plotting to save the world with the others including using her own husband, Aita as a test subject and he eventually became unstable and asked her to Euthanize him which she did, but not before somehow saving his consciousness and starting a cycle of reincarnation as a Sage who’s soul and consciousness is continuously reborn as a new person in a different time and place.
Later Juno's motives changed to wanting to rule the world instead of saving it. Her treachery was discovered and she was imprisoned (and possibly executed or left to die in some sort of prison, yet she survived and endured and began to work on making her plans become real).
At the same time (we’re talking about interactions with future Assassins, Desmond through Ezio and Desmond personally), Minerva wanted to save the world, save civilization from another cataclysmic event by working with surviving First Civ. members and humans (Eve is likely to be one of those) and communicating with future Assassins to ensure her message is delivered in a more direct way in a closer date to the date of the 2012 Solar Flare.
Minerva knew what Desmond will choose (she was present when he made the decision to heed Juno’s plan), and she could’ve seen through the Eye what will happen when Juno is set free and at the same time she saw how strong Eve was and how she was able to defy a superior civilization of God-like beings, so nobody could ever be as ready as someone who had done it before. She uses Eve’s consciousness to start another never-ending cycle of reincarnations for Eve herself to ensure that when Juno is set free, someone will be there to pick up the torch and start the revolution again.