My take: Thugs blackmailed and sexually abused the priest to cover up what was happening with the kids. The one boy who loved the priest went yandere and killed the thugs. But he died too. So, who actually killed the thugs? The boy or the priest? It's probably more basic, but that is my theory.
Also, getting esoteric, it's about the end of innocence and what can happen to an innocent soul, destroyed.
I thought the boy killed them. at the end it looks like his shirt is stained with their blood
He did. To protect his "Father". It was basically the two trying to care for one another when all their is, is the same damn repetitive circle of blackmail, sex and death. It was my understanding that at some point the boy may have died (been killed. )
Dont get the storyline of 4) Father... I kind of have the gist of it though.