I'm struggling hard with the story of this game

[Nacre]

Wanted to ask for help so I can stop trying to puzzle this out on my own.

So I beat the game, found the final boss I didnt know I was looking for, found the final final boss I didn't know I wasn't supposed to know about, and I'm still scratching my head about what just happened.

the story as I understand it: So we're the malformed spawn of god and void, created to slay those who are empowered by the flesh and blood of fallen gods and reclaim that strength for ourselves, also something something RED STAR . Along the way we learn about the history of the city, some theories that the city is the entirety of the world, that nothing exists beyond, but also there's the expedition that clearly came from outside so you can't trust journals you find on the ground from a billion years ago. Learned that the RED STAR was summoned to here inadvertently by the void scholars as they tried to gaze into the abyss.

The heralds are also not the first? There's been heralds before, and they follow a pattern of some sort? So the game is just one cycle among many, unless you get the super final boss who has some significance to something or other, maybe

[Nihtskia]

There's a lot left unexplained or just ambiguous. This is the summary of the story as far as I can tell, judging from the journals, compendium, dialogue, etc. Obviously, spoilers follow:

1. Some time long ago, beings known as the progenitors appeared within the waters of near/on a certain archipelago. These progenitors began to create things and mold the archipelago to some unknown ends (if they even planned anything at all).
   
2. People arrived on the archipelago and discovered the progenitors, who they regarded as gods. They started worshiping the progenitors and began constructing a great city on the archipelago.
   
3. The people of the archipelago discovered that consuming the progenitors' blood (ichor) granted them power and evidently knowledge. The city grew rapidly, using this ichor as its primary currency and a major source of sustenance - basically everyone in the city was consuming ichor.
   
4. A pair of sisters rose to prominence within the city, these two would later be known as the Astronomer and the Vizier. These sisters sought to better understand the progenitors and the world, and to this end constructed a great observatory (the obsidian observatory).
   
5. As the Sisters and their followers continued to study via the observatory they became aware of a strange alternate plane of reality that had seemingly limitless power and potential (the Void). They discovered a way to force open a gate to the Void and started harvesting its energy to create powerful relics and perform wonders. This led to even greater prosperity for the Grey City.
   
6. Opening the Void had side-effects, starting with the appearance of a strange, mycelium like substance that started spreading through the observatory and eventually the surface. (those white strands we see in game - the strange pale "plants" we can encounter on the surface and choose to kill or give divine remnants seem to be part of this mycelium). Later other creatures found their way to the Sister's plane via the void.
   
7. The Sisters continued to experiment with the Void. One of these experiments involved taking a stillborn baby girl's corpse and placing it in the Void. The baby (Namun) resurrected while within the Void, and gained an innate powerful understanding of life - this is the first of the three siblings you encounter in the temple (the one who activates the salt containers and tracks your HP increases)
   
8. Encouraged by their success. The Sisters continued their experiments with the Void, this time placing a living child (Rahtek) in the void. Rahtek did not gain an understanding of life like his "sister" Namun, but rather learned to wield the Void as a weapon and came to understand it as and all-devouring conqueror. However, his power continued to grow so rapidly, and his philosophy seemed dangerous enough that the Sisters intervened, sealing away his power in four vaults. (Rahtek later serves as the figure tracking your damage output increases and demanding you open the vaults).
   
9. More curious than before, the Sisters placed yet a third child into the void, (So-Venat). This child was too young to understand what was happening, and was terrified and lonely at being put in such a strange, dark place. Yet he learned to draw solace from the Void, apparently interpreting it as communicating with him. When he returned from the Void, his command of Void energies was unmatched among mortals, and he remained in the Observatory with the Sisters, further honing his skills. (in game, he serves as the figure in the pyramid that increases your void charge when you bring him void rods).
   
10. The Sisters' research continued, and at some point they gained the notice of something (the First?) Whatever this was, its focus took the form of a red star whose light changed and molded whatever it touched. One child was outside when the red star appeared and was hit with a "shard of the firmament" granting him quasi-divine power. In the aftermath of the star's appearance, the desperate populace captured this child and used him as a battery (this is the Sky Child).
    
11. The red star made living on the surface impossible (those who remained were unmade or reformed into something entirely different), so the populace of the city retreated below the surface, save those in the observatory.
    
12. The timeline gets a bit fuzzy here, as it seems a lot happens after the red star appears. The star ends up occasionally vanishing, then reappearing a hundred years later (these events become known as "emergences") it's not clear if the following events all happen in one emergence, over several emergences, or between emergences. At least more recently, between emergences, ice claims the archipelago and everything inside goes dormant, only for the ice to thaw, the ichor to flow again and all the dormant creatures waking when the red star reappears.
    
13. One by one, the progenitors vanished or died while the red star shone. They left behind "husks" filled with ichor, which the city continued to rely on.
    
14. Confused and bereft of their gods, the citizens of the city ended up splitting between two factions - one that continued to worship the progenitors, believing they must still exist somewhere under some form, while others shifted their faith to the Red Star. Among those who took the latter path was the Council of elders (first boss) and Uut the Screamer (hidden boss). This led to conflict within the city.
    
15. The gardens within the city began to change, native flora and fauna becoming monstrous, and the plants losing their vibrancy and color. The alchemists who worked in the garden called Namun, who, with her understanding of life was able to instruct them in producing "salt" that embodied life, by using corpses placed in special vats.
    
16. At some point, the scholars of the city noticed that not only where their gods gone, the ichor which granted near/actual immortality was draining away into the caverns below, where it was collecting and forming a massive glowing gem they took to calling "nacre." (This is the same glowing gem you can see in the deepest room of the Commons and the deepest room of the Bazaar). This nacre could not be used by mortals, so the city set a group of sages to monitor the ichor and try to intercept it before it reached the gem and fused to it.
    
17. While most of the sages did their best to contain the loss of ichor, one eventually abandoned his duty, instead watching over the nacre and seeming to further its growth. As the sage did so, it's form changed into something inhuman. This being would later be known as "the Watcher."
    
18. It's not clear when this exactly happened, but at some point the queen of the Grey city gave birth to a son. This son was an incredibly picky eater, refusing even delicacies from over the oceans and slowly wasting away. Finally, in an act of desperation, the royal family ordered that flesh be carved from the husks of the progenitor and fed to their son. This actually worked, and the son gorged himself on the progenitors' flesh, which slowly changed him until he eventually became "the Pustulant Prince"
    
19. Presumably under the red star's influence (again, it's not clear if this was the first emergence or a later one) catastrophe struck the Grey city, causing cave ins and bringing mass destruction and death. In desperation, the people attempted to flee to the Royal Palace, the strongest structure in the city. Some made it, but the nobles inside were quick to seal the entrance to prevent the calamity from reaching them, so many commoners "died." However, thanks to the consumption of ichor, these people did not stay dead, but rose as undead (mostly mindless ones that acted only on vague instinct).
    
20. During or after this, the Vizier left the Observatory, retreating into a mirror dimension of her own creation, where she would devote herself to recreating the Grey city at the height of its power from her imagination alone. However, over the centuries, her memories faded, rendering this task impossible.
    
21. Meanwhile, in the Observatory, the Astronomer drew false conclusions about her sister's disappearance and began worshiping the red star as well as studying it. She led others in this practice as well, and the star eventually warped them into Mutinants with unnatural powers, with the Astronomer gaining the most power of them all (and becoming the boss we face in the Obsidian Observatory).
    
22. Safe within the walls of the palace, the nobility passed the time seeking new pleasures, while living off the ichor and flesh gathered from the husks of the progenitors. However, over time, these resources were depleted and the palace fell into chaos. The inhabitants rose as undead with only passing resemblance to the people they once were.
    
23. In an act of desperation, Namun and her followers built the Ovum, a container to incubate a mix of divine ichor and pure void energies, hoping this would form something that could rescue the city. This ovum later "births" the Voidwrought (player character). (It's not clear when exactly the Ovum was created, or how long it took for the Voidwrought to achieve consciousness).
    
24. The gardens also fell into disarray and the vats stewed with the bodies they contained. This eventually led to the "birth" of a sentient plant (Achretis) who claimed the gardens as his own. It also led to some of the refuse that contained flesh from the progenitors becoming new life (the Fermented/water boss)
    
25. Over the next who knows how many centuries, the archipelago went through cycles of the red star emerging, then vanishing some time later and not returning for another 100 years. With the archipelago going dormant whenever the red star was not present.
    
26. Emergences would draw scholars and those who followed the religions based around the progenitors to either study or consume ichor. One of these groups of outsiders came to the land in a great, metal vehicle and began gathering artifacts. Among other things they gathered some of the flesh of the progenitors. This began to fuse with the vessel itself, becoming the Eternal Engine.
    
27. Either from the Eternal Engine or via the red star's influence, the crew of the vessel were transformed. Soldiers mutated into blunderbusses, commanders into command cysts, crew members into eldritch facsimiles of their original bodies, and worst of all, those that had handled the progenitor flesh were warped into the lunatics.
    
28. At the beginning of what would end up being the last emergence, the Voidwrought was "born" from the Ovum, and tasked by Namun with destroying all those who have taken the progenitor's flesh (the heralds). She seems to believe this will restore the city to its former glory and reestablish connection with the gods.

Now, this part is speculation based on reading between the lines of dialogue, compendium notes, etc. But as best I can tell is why the Voidwrought has to fight the First.

• Long before the progenitors or the Grey City, their existed a being that would later become known as the First. It encompassed all things, and bore a consciousness that spanned the cosmos. However, somehow it died. It's consciousness was cast into the Void, and its body fell to pieces. Some of these pieces would later recombine, forming pale imitations of the First, these were the progenitors.
  
• For eons, the First remained trapped in the Void, then the Sisters opened a gate to the Void. The gate was nowhere near capable of allowing the First to escape, but it did allow the First to influence the material world. Either under this influence, or acting on ill-thought out curiosity, the Sisters opened more gates to the Void, until the First was able to put much of its power forth in the form of the red star.
  
• The First also created or sent forth the envoys, who would, via haunting melodies they played, obscure the First's true presence while it slowly reformed and reemerged onto the material plane.
  
• Using the red star, the First tried to shape the world to its liking, while one by one eliminating the progenitors that had been born from its corpse. It caused the ichor, to start flowing into the caverns deep under the city, forming it into a shell for the First's rebirth (the nacre).
  
• This effort exhausted it, and at times it would need to rest within the Void for a hundred years. This was the time between emergences. Yet after it recovered it would start again, continuing to build the nacre shell that would be its egg. Either via influence from the First or by their own awe at the being, one of the sages set to prevent ichor from joining the nacre aligned themself with the First, becoming the Watcher.
  
• Because the progenitors had been formed from parts of the First, its influence was misinterpreted by many of those in the Grey City as the presence of their old gods. Under this misinterpretation, Namun sets the Voidwrought to kill off the heralds who have consumed progenitor flesh, assuming that gathering the flesh and ichor in one place will revive the deities. This is partially right, the issue being that doing so will resurrect the First.
  
• After defeating the heralds, the Voidwrought becomes aware of a divine power coming from the nacre, and is able to use keys attuned to the progenitors to establish a link between it and the Grey Pyramid.
  
• Traveling through the link, the Voidwrought arrives on the nacre, where it encounters the Watcher. The Watcher, desiring to prevent interference with the nacre attempts to annihilate the Voidwrought and fails.
  
• If the Voidwrought had not killed the envoys, their music still obscured the First, so the Voidwrought assumes the Watcher was the one undermining the city and preventing the progenitors' return. This leads to the Voidwrought destroying the Watcher for good by sacrificing itself.
  
• If the envoys are gone, the Voidwrought realizes there is a presence within the Nacre, absorbs the Watcher's power and uses it to enter the First's hiding place, where it encounters the still-reforming First.
  
• The First, not at all keen on having its resurrection denied, attacks the Voidwrought, but ultimately fails, at which point the Voidwrought absorbs it.
  
• After absorbing the First, the Voidwrought seems to stay in the Void. With the First gone, it's influence in the form of the red star vanishes, never to reappear. The Voidwrought also seems to absorb divinity from the ichor and progenitor flesh, allowing death to come to the Grey City, both to the undead and the monsters within. This done, the Grey City is now safe for explorers and scholars to descend upon it. Which we are told happens in the ending text.

[Nacre]

Originally posted by Nihtskia:

thank you, 1 and 3 were completely unintuitive to me. something something gods showed up, did something something, people SOMEHOW started eating them. I thought there was more that I just hadnt found a journal about but no its just... that. All the subtext speculation about the First making the Red Star would have never occurred to me. glad to know the tangled knots of the story are actually just knots and not my own misunderstanding