From the top of the chapter 1 page:

This is not a strict single-point-of-departure fic - there exists a primary point of departure, at some point in the past, but also other alterations. The best term I've heard for this fic is "parallel universe".

We'd previously assumed that the primary point of departure was when Lily Evans/Potter used magic to help make her sister Petunia attractive enough to get the attention of Michael Verres, who raised HJPEV in a much better environment and gave him a much better education than canon!HP, which caused HJPEV's increased intelligence. This was even reinforced by Petunia's comment that "...Lily would tell me no, and make up the most ridiculous excuses, like the world would end if she were nice to her sister, or a centaur told her not to..."

However, it now seems that the reason for Harry's increased intelligence was that he had parts of Voldemort's mind implanted into his own when he was one year-old, presumably years after Lily helped Petunia. While HJPEV's intelligence isn't the only thing in the story, without that link I don't see how Lily's actions were the primary factor in determining HJPEV's potentially apocalyptic course of life.

Thoughts?