User blog comment:Aegis Runestone/Hi, It's been a long time. Would anyone like to catch me up on AC?/@comment-2112031-20170529200159

Unfortunately, a lot of the stuff mentioned at the end of Brotherhood still hasn't been followed up on, leaving us with unaswered questions.

If you complete the Rift puzzles, Desmond will have a confusing conversation with Desmond where, among other things, he says: "The sun, your son..."

Which is now accepted as referring to his actual son.

From what I understand, Minerva's recording in the Vault was made before she discovered that Juno had tampered with patterns of "the Eye", which is why she changed her mind about Desmond using it.

Sages are human reincarnations of the Isu Aita, Juno's husband. Basically, Aita volunteered for an experiment which involved transferring his consciousness into another vessel. It failed, putting him into a catatonic state and requiring Juno to eventually euthanize him.

However, Juno eventually devised a plan to add samples of Aita's genetic code into human DNA, which resulted in humans being born every so often with Aita's genetic code, having his appearance and eventually unlocking his memories. Some Sages are completely consumed by Aita's memories and become loyal to Juno, whereas others struggle with their dual memories and try to resist it.