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Okay, I had this theory that I wanted to discuss. In ACIII, when Juno explained the ways they tried to save themselves from the impending solar apocalypse. She stored her mind in the Grand Temple, by inputting her thought patterns and the like in its walls and structure or wherever. When Desmond "died" and he saved Earth and freed Juno, how could she return without a physical body? I think when Minerva told Desmond would "die", she talked about his thoughts, his personality, everything that made Desmond Desmond. And that got replaced by Juno. So Juno took over Desmond's body. At least, that's my theory. What do you think?