Are all the enemies crazy monsters? Some of them look like normal humans with weapons, why are they fighting the Penitent One?
The Penitent One was part of the Brotherhood of the Silent Sorrow, who came into conflict with and were excommunicated by His Holiness Escribar, head of the Corrupt Church and the final boss. It's likely he has plenty of people who serve him of their own free will, and it would make sense for them to target a member of an order that's been declared heretical.
Was there magic in this world before the Miracle? Was it a fully unique event and the world was like our world beforehand?
What exactly is the true nature of the miracle? It was created by the High Wills to perpetuate the cycle of martyrdom in Cvstodia but it is also through the power of the miracle that the means of ending the High Wills is born.
It's possible that it basically runs on automatic, while it is "Their" power, they can't actually control it's effects, hence why they had to work on Cvstodia to make it a Martyrdom Culture to the extreme, so that someone like the Penitent One would have a low chance of actually gaining the power to actually fight them. It's also possible that it was the combination of everything the Penitent One gained throughout their journey, the exact right combination of separate "blessed" relics and the like, to actually be able to cause harm to the High Wills.
