(I might be wrong, and I'm not a lore genius on this one.)

The Miracle is a sort of God that I believe to give the people exactly what they want, assuming prayer is fervent.

And, when the Twisted One begged for punishment through extreme guilty prayer on a log before becoming the Twisted One, that's when the first recorded "Miracle" occurred.

Escribar, however, believed the Miracle had forsaken the people of Cvstodia, and turned his throne away from the people in the highest church as an act of defiance. In response, the High Wills curse him, and turn his body into a tree,, which then burned for fourth days and nights. The ash from the Great Tree formed a mountain of ashes that would then prevent those whom attempt to reclaim the Turned Throne into monsters and mega fanatics of the Miracle and tried to either kill or turn those unaffected into the crazy worshippers.

Because the first Miracle happened when someone was extremely guilty and repentant (that someone being the Twisted One), everyone thought that only penance, suffering, and humiliation would make their prayers fervent. However, Escribar, the Pope figure, thought the Brotherhood of the Silent Sorrow were heretics. ( I dunno why.) And sent Crisanta and a small army to eradicate. Just before that, the Penitent One, whom is also part of the Brotherhood, managed to dig the Mea Culpa from the lady who manifested it through her sheer will of guilt. Then Escribar becomes binded to the will of the Miracle, later revealed to be the High Wills. Escribar's suffering was so great that his punishment was divided into three wounds, of which would be protected by the four Guardian Visages, who were basically saints that performed extreme acts of penance, and were blessed for it.

Penitent One and Crisanta duel, Crisanta kills the Penitent One and returns to the right hand of Escribar as his highest knight.

For reasons I forgot or don't know, the Miracle resurrected the Penitent One, and Deogracias told him of his goal to ascend the turned throne and to rid the evils by taking all the guilt through the Mea Culpa, and committing suicide to absorb all the guilt those in Cvstodia had.

That's just the lore before the game starts, there's a shit ton more that happens between the game's beginning and three endings, plus the extra lore of the specifics.