My guess would be is the two sides White and Black are supported by two separate sides White being the Sages and Black by the Shadow Triad. I believe Ghetsis is apart of the Black Plasma as Shadow Triad helped him bust out of jail. And the White may be the people that don't agree with his way of "freeing" pokemon now that they know his true intentions. I am sure the White would like to rally around N but now that he is missing they are in somewhat disarray. N could back the White side once he comes into the picture and then face off with Ghetsis the Leader of the Black side too finally end their "feud" so to speak.
Seems like it will be Magma/Aqua like to me. Too sides clashing against to separate but similar ideals.