The TSAB High Council. As of the end of A's chapter 12, they are giving Gil Graham two days to obtain the Book of Darkness. If he fails, they have implied that they will make something happen to Equestria. And if he refuses, they imply that something equally bad will befall someone Graham cares about. And when he finally caves in and does do what they want by freezing Trixie and the Book (for a few minutes), they proceed to A) forcibly assume control of the Arthra (including holding Lindy hostage), and B) decide to go ahead with their contingency plan - obliterating Canterlot from orbit - anyway.
Nachtwal killing the Wolkenritter. Even moreso than in canon because the canonical one was more misguided/corrupted than the openly hateful, omnicidal one here.
The Woobie: Fate in the first part, as per canon. Trixie in A's.