Things are getting really interesting now. I look forward to what you do.

Stygian found his notes, didn't he?

“I want you to to be ready to retreat to Everfree if things go badly. I know I can hold them off long enough for you to rally an army of your own to match it, but only if it goes to the point of fighting is the only option.” I said as seriously as I could muster.

Its literally the only option.

“I'm going to surrender to them, perhaps I can avoid any more bloodshed.” I said with my gaze on the floor.

That makes absolutly no sence

Sooo... Did the Minatours kingdomfuse with Equestria via Marriage?

10884494
Maybe became a junior partner.

So the one who stole Ed's research notes was either stygian or starswirl. Considering how he said it was someone he trusted I'd have to say starswirl.