In the original plot, the pc:s are supposed to seek out the Shoanti to learn more about the Midnights teeth - Neolandus have told them quite a bit about it, but he don´t know what to do about it. That´s it.
I plan to run it this way instead:
1. Neolandus doesn´t know much at all about what the Queen has found/has become. He suspects it is something evil found under the Grand Mastaba, something the Shoanti was guarding up until they had to abandon the pyramid. I think this is more exciting for the players - WHAT is it thats been loosed? How shall we stop what we don´t know much about?! (This is the standard way for me to deal with stuff like this - remember the horror movie is almost always more frightening before the nature of the horror is reveiled.)
2. The pc:s need to unite the Shoanti to build an army against the Queens forces, to save Korvosa.
I set up a grand animosity among the three Shoanti tribes, and the Skull clan already has infighting about wether to attack Korvosa again, after what happened to Gaekhen in EoA. Thoasand Bones has been able to stop futher attacks - a war versus Korvosa with only the Skull clan would be won by the Queen.
This also sets up for an alternative epic ending with the pc:s doing their thing AND a grand battle outside Korvosa between the evil forces and the Shounti.