@Kanpachi: i feel that Akane's ability to be places in which she shouldn’t exist, like the fact that she was present on the second nonary game, even though she was dead on that timeline, will be key in the next game. I believe she did this whole thing because she can see a ending where she can prevent, because of that ability, this whole unfortunate set of events from unfolding, and that way stopping everything that happens in all three games in a way that makes it clear to the player that the other timelines get erased or never happen, at which point the horrible things she did also don't ever happen, and maybe you get a version of Akane that marries Junpei and lives happily ever after. This would be the best possible ending for the series, from a happiness point of view.
The other possibility, that would be more dark, is that she does all this to try and finds a perfect ending for her, while leaving other horrible timelines that were created as a result of what she did, this would mean that maybe the best ending for her isn't what is best for everyone, and the third game revolves around you stopping her, and fixing the timeline by erasing these horrible realities she created, and in the end creating a one true timeline, but one not so rosy as the other option, one where Akane's death, and her non revival through the second nonary game, is key to saving mankind.
Anyway this is all speculation and by the amount of incredulous shouting i did during both those games when twists are revealed, i believe trying to predict the plot and twists that expects us all in the third game is mostly pointless, because they have way crazier things in mind, although i will admit it is fun.