The plot continuing here is the White Tower Conflict. We know that:

a) Elaida is ambitious, not a Darkfriend

b) Elaida is a Black Ajah puppet, chosen because she had reason to hate or at least distrust Siuan as Amyrlin, and because if she ruled then there would be no links to the Blacks.

c) Egwene has to take over the tower, after all, she's the heroine here!

d) From the testing Ter'angreal, there will be the Great Purge during which the Black Ajah will be destroyed

e) Elaida will 'unite the tower beneath her'

f) Elaida is about as scared of the Black Ajah as everyone else.

So, in Book 9, I believe that Elaida will discover that the Black Ajah has duped her and used her as a puppet Amyrlin. So she gets in touch with Egwene and together the White Tower united, under Elaida (She knows about the Black Ajah after all, and no one else except those Reds, whose names escape me, do probably) This fulfills all except for (c). So, Elaida leads the Tower and probably dies tragically killing Alviarin or Mesaana (more likely Alviarin). She becomes a hero, and we actually finally see the Red Ajah painted in a good light. (They aren't ALL Darkfriends!) Then, because Egwene is (as I said) the heroine, she becomes Amyrlin. This fits in with everything we know. most of this theory is what I'd do if I were writing it, and logic, but it is also dependant on whether or not the Ter'angreal's vision of the future is true or not. I say yes, because most of the rest of Egwene's vision (becoming Amyrlin and the Tower splitting, etc) and Nynaeve's vision (marrying Lan) have happened. So, this seems quite likely.