The story gets to the point where it is stated that the enigmatic leader of the Sorcerers of Zero was probably the one who started the plague that ended up getting Sorena burned at the stake, and also the one who killed everyone in the caves and stole the Grimoire of Zero.
But it is then revealed that the enigmatic leader is actually
Thirteen, who has been pulling the strings on both sides all along.
But this guy is a seriously impressive sophist and gives contradictory responses to Zero at every turn. And when actually confronted about the killing everyone and stealing the grimoire, all he says something like, "The people in the caves were the same dead or alive." But this could also be taken to mean that he had no reason to kill them, and now I don't know whether he did or not. And the conversation dies there with no further explanation on it. Not only that, but Zero and him seem cool at the end, which would seemingly be odd if he murdered everyone they knew.
It is both stated and shown that the plague was accidentally caused by two apprentice witches conducting an experiment.
Once again, Thirteen's sophistry is on full display when he denies having orchestrated the witch's rebellion with the intention of quelling it. He claims he taught them magic in the hopes that they would use it properly, and it is simply that they strayed from the path that led to these events.
Who killed them? Are the light novels clearer on this?