In FromSoftware's Lovecraftian horror-scape, the games industry was introduced to a fresh hell of eldritch creatures, mysterious organisations, and wayward NPCs. The Healing Church is at the forefront of Bloodborne's story and their actions inevitably led to the events of the game. The story is cryptic and enigmatic, but after putting the pieces together it becomes clear that the Church have more than a few skeletons in their closet.
Indeed, they are responsible for more than a few heinous acts throughout the story, having kicked off everything from the scourge of the beast to Yharnam's interaction with the Great Ones. With no shortage of crimes to choose from, these are the worst things the Healing Church is responsible for.
6 Communing With Ebrietas
Described as the 'left-behind Great One', the Daughter of the Cosmos rests below the Grand Cathedral, docile and idle. While exploring the Upper Cathedral Ward and the Orphanage, it can be discovered that the Choir-a high ranking branch of the Healing Church, as stated by the description of their garb-have been keeping Ebrietas hidden away so they could commune with her.
Presumably they hoped to become enlightened on how to beckon the Bloodmoon and make contact with more of the Great Ones. Exactly what they did with the Daughter of the Cosmos otherwise is uncertain, but it can't have been anything good.
5 The Orphanage
The Choir were not only responsible for interacting with Ebriertas. They also saw to what happened at the Orphanage, a place that is riddled with beasts and cosmic horrors when the player finds it. While once presumably functional as an actual orphanage for the children of Yharnam, there are no humans left here. There are, however, an abundance of foetus-like monstrosities slithering across the ground as the player passes by.
While unconfirmed, it appears fairly explicit that the Choir experimented on the children there and turned them into the Celestial Children seen around the area, possibly using the blood of Ebrietas to do so.
4 Iosefka's Experiments
Early in the game, the voice actor for Iosefka changes and an impostor actually takes her place. Should players bend to their own curiosity and investigate the clinic later on, they will find that the real Iosefka has become a Celestial Emissary and the impostor is responsible. She gives the player a chance to turn around and leave her to her research.
If they agree, they can send some NPCs here for the impostor to turn into more of the otherworldy creatures. The logical conclusion is that Iosefka was conducting these experiments on behalf of the Church to try and make contact with the Great Ones, likely working as a member of the Choir who were performing their own experiements at the Orphanage.
3 Laurence Leaving Byrgenwerth
Though his departure from Provost Willem technically takes place before the existence of the Healing Church, Laurence would go on to found the organisation based on the concept of blood ministration. After discovering a holy medium in the labyrinths underneath Yharnam, Laurence informs Willem that he will be parting ways with Byrgenwerth University.
His deformed and beastly skull is found in the Grand Cathedral, a result of his decision to dabble with the blood found in the labyrinths, and his beast form before his demise can be fought in the DLC. Because of his decisions, the entirety of Yharnam went on to suffer from the beast plague and the Healing Church continued to commit atrocities in the name of progress. Thanks, Laurence!
2 The Research Hall
In the Old Hunters DLC, the player travels to the Hunter's Nightmare to discover even more about the events that lead to Bloodborne. It takes place in a different form of reality, but this Nightmare has clearly been modeled after Yharnam during a time when everything was beginning to descend into chaos. In a secret area not accessible in the vanilla game's Yharnam, a research hall is found with dozens upon dozens of helpless victims strapped to beds and tied up in straight jackets.
Their heads have become bloated and bulbous, reminiscent of the creatures found in Iosefka's Clinic. They probably served as precursors to the Celestial Emissaries as the Church attempted to perfect them, as did the Living Failures that serve as the DLC's more forgettable boss fight.
1 The Fate Of The Fishing Hamlet
When players come upon the Fishing Hamlet at the end of the DLC, the residents are deformed and have become some horrific hybridisation of man and sea creature. The reason seems to be the presence of Kos, a true Great One that has washed ashore nearby. The entire scene takes inspiration from the story "The Shadow Over Innsmouth", where a similar situation unfolds after the town's citizens discover an old god slumbering in the ocean.
The extent of the Healing Church's involvement in the situation is debatable, but the presence of Brador-who seeks to keep the secrets of the Church under wraps-and Simon the beggar imply the Church had been there for quite a while, to either study what was happening or take part in what became of Kos. Whether they had anything to do with the Orphan and its creation is not addressed enough to say for sure. But they undoubtedly inspected its mother's corpse for their own gain, sparing not even a thought for the child or the deformed villagers.