Nobody really knows exactly what the main story is. The main gist of it seems to be:
You as the player go for blood ministration (why is never established; perhaps you are suffering from some kind of disease, or maybe you’re just chasing a high) and presumably make an enquiry about “paleblood”. I hope it’s not too much of a spoiler-within-a-spoiler to say up front that exactly what paleblood is is also never established.
So you have a nightmarish vision and wake up in a world overrun with beasts and near beasts. Apparently the whole thing started with the college of Byrgenwerth somehow finding the Pthumerian labyrinth, which led to Laurence and pals discovering a “holy medium” within. Exactly what this holy medium is is never established (sensing a theme?), but opinions range from Ebrietas, which makes sense, to Queen Yarnham, which also makes a kind of sense, to one of the Pthumerian chalices, which makes less sense in context but has echoes of the grail. Anywho, it turns out that this blood does bad things in addition to good. My read on it, thematically, is that the blood, like Bill Cosby’s cocaine joke, intensifies one’s “true nature”. Most men are beasts at heart, so beasts they become. The church quietly employs hunters to clean up the beasts, until it all goes not so quiet with Old Yarnham. There’s quite a bit of convolution with the Church Hunters and the Old Hunters and the Executioners, but I don’t think a solid grasp of it is really necessary to the basic story. The hunters find themselves falling behind in the arms race, so they take blood and become mad with it themselves and so hunters of hunters are brought in and the snakes eat the lizards and the gorillas eat the snakes, etc.
So much for the early stages of the game. After you reach Byrgenwerth things get weird. Well, actually in the woods, I mean what’s up with those snake guys? Some obscure bit of lore having to do with the Madaras brothers, apparently, who were hunters with a giant pet snake. Anyway, unimportant. Byrgenwerth is where it all began. They found the labyrinth under Yarnham. In keeping with the game’s Lovecraftian themes, there was of course an Elder Race, the Pthumerians. The Pthumerians, apparently, worshipped the Great Ones, and this intrigues Byrgenwerth, especially provost Willem. He sees an opportunity for mankind to “advance,” apparently. So they plumb the depths of the labyrinth looking for things. This is where the aforementioned “holy medium” comes from. For reasons the exact nature of which are never established, perhaps experiments gone wrong, Willem distrusts this holy medium and the blood it provides. Laurence, Willem’s student, respectfully disagrees and takes off to form the Healing Church, using the blood to perform, one assumes, miracles of healing. And also make beasts, oops.
So Willem was right about that, but his own ascension plans go rather awry, too. He braindeads himself in the search for “more eyes” and ends up turning his students into Cronenbergian monsters (how exactly is, I should copy and paste this phrase, never established), including Rom, whose precise function in the world is rather fuzzy.
She “hides” all manner of rituals. After killing Rom, the blood moon is revealed. The same blood moon, we are told, which shined on Old Yarnham before it was burned to (imperfectly) hide the sins of the church. This is where things really get fuzzy. Suddenly we are introduced to some guys named the School of Mensis. They are also, I guess an offshoot of Byrgenwerth? But instead of blood use they more directly follow in Willem’s legacy and attempt through some kind of ritual whose precise nature is never really established to contact a great one directly. Which great one? Mergo.
Who the heck is Mergo? Mergo is Yarnham’s child, perhaps with Oedon, whose chapel is the hub for Cathedral Ward. Mergo was stillborn, since “every great one loses its child,” which really makes you wonder how they keep going as a species (but are they a species? maybe not), but that didn’t stop Mensis, but their contact, tragically, goes awry. Most of them appear to be regurgitated from the nightmare lands as the One Reborn, but their brains, I think, all get glommed together as the Brain of Mensis. Except Micolash. Uh anyway, inside of the nightmare is Mergo, or what’s left of him/it. You fight his wet-nurse and put an end to Mergo’s tragic existence in the nightmare. Then one of three things happens:
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You choose to die one final time, in the Hunter’s Dream, and wake up in the real world (maybe? Probably?) the hunt over, the night ended, and you happy and healthy (uh maybe).
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You choose to stay, in which case Gehrman causes a ruckus and when you kill him suddenly the Moon Presence appears and makes you Gehrman Mark II: Bloodlectric Boogaloo, appointing you to look after the dream.
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You were incredibly inquisitive during the game and made some profound leaps of logic, or you followed a wiki, and you found and used three (of the four, whoops) special items scattered around the world and when the Moon Presence goes to embrace you it is repelled. A terrifically easy fight ensues, and then. You turn into a slug.
So what does it all mean? I am tempted to throw up my hands like JK Simmons in Burn After Reading and say, “Fuck. I don’t know.” However, it seems as though the Moon Presence was using the hunter to eliminate Mergo for some reason. Mercy? Rivalry? This is never established. To eliminate Mergo, it was necessary to eliminate Rom (to reveal the way to the nightmare). Who is the doll? Some say the incarnation of Formless Oedon, and in saying, “Ah, you’ve found yourself a hunter” she is speaking to the Moon Presence, possibly derisively. In walking the hunter’s path, the player’s character gains more and more insight and more and more power, eventually gaining the ability to challenge the MP and ascend to great one status him or herself. This only happens if those three items, which various other characters in the game tried and failed to use, are found and used. Oedon (if the doll, who knows) doesn’t seem to mind this. Perhaps it even welcomes it, making you a true surrogate for poor Mergo. The hunter’s fitness for this whole thing is established at the beginning, I take it, when something within him or her rejects the beast scourge, which prompts the MP to send the messengers to spirit away the hunter to the dream. What exactly the messengers are is never established, but there are, of course, many theories.
To sum up: you take some blood and have a hallucinatory adventure revolving around inscrutable cosmic monsters possibly having some kind of family feud, and if you play your cards exactly right become one of those inscrutable cosmic monsters yourself.
One of the overarching themes is, fittingly, inscrutability. Why do the great ones do what they do? Who knows. Where does Kos fit into this? She, uh, doesn’t, really, which is too bad. Where do the Vilebloods fit into it? They don’t really, either. The vilebloods I can understand as a kind of earlier draft of where they wanted the story to go, maybe. You can see hints of the Child of Blood being important to things, hints that eventually lead to nothing. Kos, on the other hand, being added 8 months after the game was released, I don’t understand. Maybe it’s a sign of where Miyazaki or someone else wanted the story to have stemmed from? The DLC has some great story beats in it, but ultimately in terms of understanding the overall story of BB I don’t think it matters.
Great, great game, by the way, although I wish the environments were just a little bit more differentiated the way they are in souls games. Much of the above I took from others’ analyses, some from my own play and thoughts both on that play and those others’ analyses.