"As Zendikar has bled, so will Innistrad. As I have suffered so will Sorin"
I’m going to guess that Nahiri is seeking
vengeance on Sorin for using her plane as a quarantine zone for the Eldrazi. It was her lithomancy and the creation of the Hedron allignment that allowed their imprisonment. So it seems logical that she would be able to alter and move these cells somehow, maybe even across planes. I think she has essentially turned Innistrad’s silver moon into a sort of Hedron, and has transferred Emrakul into it. As someone else said with the
Delirium and Madness mechanics, Emrakul can influence biological entities, and with the moon casting his “shadow” over Innistrad this is entirely possible. However my biggest clue in this theory is simply the set releases in conjunction with the change of expansions to two set blocks.
First, during
development Shadows Over Innnistrad was intended to be the third set of the Battle for Zendikar block, before the change to two set blocks was made. With Ulamog being the big bad in BFZ, and Kozilek in Oath, we’re safe in assuming Emrakul is on his way. However, because of this change I don’t think we’ll see him until the second set of SOI, which is also my second clue, because it’s called…
ELDRITCH MOON