Lore

King statues
There are a number of statues of the king scattered around the island, notably in the Promenade of the Condemned, in the Stilt Village and in the Graveyard.
 * There is a statue of the King in the Promenade of the Condemned. The Beheaded wonders how he can see with a helmet covering his face.
 * Close to this statue and in other areas of the island, there can sometimes be another, desecrated statue bearing the inscription "We'll skin you alive". A cow head lies beside it, emblazoned with the King's coat of arms, which shows that some citizens were violently opposed to the King's policies. He then turns and says: "What a brave and courageous message". This shows the Beheaded agrees with the people.
 * Another statue in the Stilt Village depicts the King with his Hand. The Beheaded remarks that the Hand of the King's statue is a little too big, as if it was overshadowing the King's. This might imply The Hand actually holds more power than the King himself.

Orders of the King
All over the island, the Beheaded finds a variety of orders written by the King. Most of these relate to the imprisonment and quarantining of criminals, infected or plain innocent people. Some of them are direct orders to high ranking public officers such as Castaing or the Alchemist.
 * A public order by the King can be found next to hanged prisoners. It orders the imprisonment and execution of all people presenting signs of abnormal behavior or physical appearance, i.e. suspected of infection by the Malaise. A bottom note in brackets adds "(if the prison doctor confirms the diagnosis of infection)", which implies that confirmation is actually not important, and that suspicion of infection is enough proof.
 * In the Ramparts and the Promenade of the Condemned, a similar order from the King addressed to his officers can be found.
 * In the Ramparts and the Promenade, an order from the King reads, "If the cells are overpopulated, use the outdoor jails or the oubliettes. Leave no suspects unsupervised." This shows that the Prisoners' Quarters were becoming full due to the imprisonment of too many people.
 * In Castaing's office in the Prisoners' Quarters, the Beheaded finds a direct, secret order from the King to the prison's warden next to a bag of money. The King asks Castaing to stop controlling the entrances to the prison until further notice, which seems to imply unlawful imprisonments and prisoner transfers were taking place on orders of the King.
 * A later secret order to Castaing, along with another bribe, scolds him for making the King's orders public. He also instructs him to not let any prisoners leave, even if they have finished serving their time.

Grimoires
The Alchemist's Grimoires are scattered around the island and recount his various experiments with the Malaise and how to cure it.

In the Sewers, the Alchemist was collecting mold and mushroom samples for his experiments. However, the increase in the numbers of revenants made his work increasingly difficult.

In the Stilt Village, the Alchemist has set up a laboratory dedicated to curing ill "volunteers". He reports that the essence of bupleurum seems to relieve symptoms, especially blood vomiting. The Sanctuary seems to have been especially important to the Alchemist's research. It's the only (?) biome that contains two different Grimoires.
 * It is unclear if the volunteers actually wanted to take part in the experiments or if they were forced.
 * The Alchemist writes that people believe the sap flowing through the walls of the Sanctuary is responsible for the Malaise, by contaminating the sewer network. He also suggests that this same substance could be the solution to the epidemic. It is unclear if the substance is in fact the source of the Malaise or if it's only a rumor. What is sure is that the Alchemist harvested and used this substance as part of a treatment for the infection, as indicated by the Grimoires of the Ossuary and the Clock Tower.
 * In another Grimoire, the Alchemist references the Time Keeper's efforts to combat the Malaise. He implies that she is manipulating time to contain the Malaise, but that her spell cannot contain it forever.
 * In the Ossuary, the Alchemist was applying the substance found in the Sanctuary on bones from corpses, likely executed prisoners. The substance's effects were unpredictable and the Alchemist reflects whether his experiments are worth killing so many people.
 * The Alchemist was also researching the Malaise in the Forgotten Sepulcher, but the darkness prevented him from continuing his work.
 * In the Clock Tower and in the Castle, a grimoire reports that the Alchemist found a formulation (which likely includes the Sanctuary substance as the base ingredient) that slows down the mutagenic effects of the Malaise.
 * In the Castle, the Alchemist was experimenting human/plant crossings, which were unsuccessful according to his notes.

The Time Keeper
Information about the Time Keeper can be found in a few lore rooms, mostly located in the Clock Tower. [More lore needed]
 * A letter left by the Time Keeper indicates that she is repeating the same day over and over, as if time was rewinding every day. indeed, the Time Keeper keeps track of all the infected people and monsters she has executed, but all her entries are classified as "Day 1". It is also implied that her task makes her increasingly exhausted, as the number of executions decreases each day.

The Concierge

 * The Concierge used to be the prison's Warden back when he was still human. He was called Castaing and was in charge of controlling the prison's entrance as well as managing prison guards.
 * Castaing received secret orders from the King to stop controlling the entrances to the Prison and to keep all prisoners inside, even those who had finished their sentence. Castaing put a public sign asking for citizens to report any signs of infection or odd behaviour, but was scolded by the King for making his secret orders public.
 * The King later asked Castaing to focus on preventing imprisoned villagers to cross the bridge and escape back to their homes, by using force if necessary. It is unclear if those prisoners were infected or not, but it seems they were not guilty of any crime.
 * Castaing became ill and his body mutated after he got the Malaise, which led to him becoming the monster known as the Concierge.
 * It is implied that Castaing was taking bribes from the King. His motivations for doing so are unclear, but it seems Castaing needed money to support his lazy, rich lifestyle, as indicated by his sunbathing crib on top of the Ramparts.
 * Castaing had a number of offices around the Island, notably in Prisoners' Quarters, the Promenade of the Condemned, the Ramparts and Prison Depths.
 * Castaing had a book titled "Directing a prison for dummies", which includes a chapter on "bridge construction", which is a reference to the Black Bridge where the Beheaded fights him.

Conjunctivius

 * It all begins with a nameless, faceless corpse in the Sewers, most likely infected by the Malaise. The body is all bloated and one of its arms has mutated into a tentacle. A green goo came out of the body and made a trail towards a small hole in the wall.
 * "The body is all bloated... One of his arms changed into a tentacle. It's as if the body had started to mutate! A viscous substance is oozing out of the body and across the floor... like a snail's trail."
 * After this initial encounter, the Beheaded finds that same trail of green goo and an empty cocoon, next to a bigger hole in the wall, which was made by an adolescent Conjunctivius.
 * "(...) This strange substance on the ground again. The trail leads to a sort of... giant cocoon. (...) The trail ends at this hole. And it's one hell of a big hole."
 * Later, the Beheaded stumbles upon the trail of green goo close to a corpse. The trail of goo leads to the remains of a huge cocoon and a gigantic hole, which was carved by adult Conjunctivius as she escaped.
 * "Still this trail on the ground. Whatever this thing is, it's pretty obvious that it... grew. Or evolved. Or mutated."
 * The corpse doesn't seem infected and wears prisoner clothes, which could imply it's the prisoner who escaped from the Prisoners' Quarters. Why he is not infected despite being killed by Conjunctivius is unclear.
 * Finally, a message left by soldiers evokes how difficult it was to chain Conjunctivius, which was likely an order of the King. This explains why Conjunctivius is found imprisoned in the Insufferable Crypt when the Beheaded arrives.
 *  Make sure you don't miss your guard duty outside the MONSTER's room. It wasn't easy to chain up. Wouldn't like to have to do it all over again! 

The Beheaded

 * The Beheaded seems unaware of how they came to exist.
 * The Spider comments that the Beheaded is an abnormality, and that some unknown "she" is looking for it..

Prisoners
Found in Prisoners' Quarters, Promenade of the Condemned, Prison Depths and Ramparts Note: Player can only see the Celled Prisoners hands which are similar in color, look, and chained similar to the merchants the player encounters in game, there are also 2-3 empty cells in the Toxic Sewer, implying that the merchants in the game were held there similar to the Celled Prisoner before escaping to other parts of the island. Found in Prisoners' Quarters, Promenade of the Condemned, Prison Depths and Ramparts
 * Tom the Mushroomologist is a prisoner who collects, studies and sells mushrooms. His cells and stash are found in different parts of the prison, which implies he was able to move around the Prison to sell psychoactive mushrooms to other prisoners.
 * Celled Prisoner (referred to as Gollum in the game's files) is a prisoner found in the Toxic Sewers, he will address the Beheaded upon the first time they approach his cell, he leads/tells the Beheaded about the rune (his rune) that allows the player to teleport.
 * Prisoner 545 died from exhaustion and hunger as he was making his escape through a spoon-carved tunnel in the Promenade of the Condemned. He did not manage to get out of the well.
 * A prisoner managed to escape his cell before he got infected with the Malaise. It could be the same prisoner we find dead in the Toxic Sewers.
 * A prisoner is found hanged in a cell full of flowers. He holds a red flower resembling the Gardener's Keys. Why he was imprisoned is unclear. A weird flower with the note "do not water after midnight" seems to be a reference to the Gremlins movie. It might be the result of an experiment with the Malaise or with infected materials.

Soldiers
The soldiers were given orders by Castaing and by the King, and left some letters to one another.
 * The archers of the King were lousy at their job, as indicated by their terrible accuracy in a "live target training" area in the Ramparts.
 * Some soldiers were panicking and wanted to abandon the Island before they got infected.
 * An order by the King to the soldiers implies that some of them were rebelling against the King and disobeying his orders. The King made it clear that dissent would be met with swift execution.
 * A letter found in the Prisoners' Quarters shows that some soldiers didn't know why they were instructed to imprison innocent villagers, and thought the sick should be treated instead of confined.

Malaise lore

 * Contaminated bodies are found in the sewers. The Beheaded wonders if those bodies are responsible for the initial infection of the citizens, or if those bodies only helped spread the Malaise by contaminating the whole water network.
 * A giant broken door is found next to a soldier message warning not to open this door, lest the rats would get out and spread the Malaise. The Beheaded remarks that it is unlikely rats made such a big hole, which implies something else was kept behind the door. The corpse of Prisoner 236 is found close by: he presumably died while trying to escape.
 * It is unclear who or what was behind the giant door. The lack of green goo trail, the fact that Conjunctivius is still in chains when the player reaches the Insufferable Crypt and this lore room being part of the "Infection" room series and not the "Beholder" (Conjunctivius' old name) series suggest that the creature which escaped was not Conjunctivius.
 * The rotten corpse of a soldier is found next to a stained letter he wrote describing his symptoms. He was coughing blood, his body was so itchy he scratched himself until he bled, had headaches, blurred vision and depression.

Prisoners' Quarters

 * "In the social hierarchy of the island, there are the dogs, the rats, and just below them, the prisoners."
 * "The lucky prisoners had a window in their cells... They ended up choking on the ashes from the Ossuary."
 * "The prison is directly connected to the outer yard. The prisoners can choose between the rats and the crows."

Promenade of the Condemned
There is a well in the Promenade which can contain a number of things.
 * "It's never a good sign, being sent to the yard. Few return. When they do, they're never quite the same."
 * "The charming countryside atmosphere of the forest has given way to a... less wholesome ambiance."
 * "Time was, you could still hear the occasional bird singing outside. Now there's nothing but the caw of the crows."
 * Sometimes, the well contains rubbish and a rotting drowned corpse. The Beheaded reflects that it's no wonder people get sick when filthy stuff gets thrown in the water supply.
 * In another instance, the Beheaded finds a prisoner who died from exhaustion and hunger as he was making his escape through a spoon-carved tunnel.

Toxic Sewers

 * "Many believed the sewers were a path to freedom. No one ever made it out the other side."
 * "The prison dumped all its unspeakable filth into the lower galleries, so it's no wonder something horrible emerged from them one day!"
 * This seems to be a reference to Conjunctivius.
 * "A greenish substance oozed its way into a number of pipes along here... and it continues to spread."
 * "Hmm... is that... is that smell normal?"

Dilapidated Arboretum

 * "Once frequented by the lords and ladies of the island, they often noted that some of the mushrooms seemed to shrink from their presence."
 * "Dappled light, soothing fountains and a fresh air brought the royals, aristocratic and various hangers-on. Unfortunately they brought the stink of the Royal Court with them..."
 * "Earthy smells of compost, spores and decay fill the air of the dilapidated Arboretum. The new inhabitants seem to like the climate quite a bit."

Prison Depths

 * "The worst prisoners were locked up here, in the company of the worst guards."
 * "Few prisoners managed to see out their time here alive. None, actually."
 * ""To be transferred to the Depths" meant you weren't coming back. All you could really hope for was that your execution would be quick."

Corrupted Prison

 * "Donating your body to science takes on a whole new meaning when you're still alive."
 * This is probably a reference to the Alchemist.
 * "The guards were the first to succumb. Unless no one noticed the difference in the prisoners..."
 * "It's unthinkable that even the stones are infected."

Ramparts

 * "To keep things exciting, the guards sometimes threw condemned prisoners from the Ramparts. There's definitely nothing worse than the screams of someone who knows they're headed for the edge."
 * "The guards would perch themselves on the Ramparts at the first sign of the Malaise... It didn't really help."
 * "Once, some poor sod tried to escape over the Ramparts... He died of exhaustion during the climb, so the guards left his body on the wall to make sure everyone got the message,"

Ossuary

 * "After the Night of the Bloody Riots, the guards decided to condemn a whole wing of the prison so they could dump the bodies in there."
 * "A thick layer of ashes covered the walls of the place. Filth crept into every nook and cranny."
 * "One of the worst places on the island... Or one of the safest, depending on who you ask."

Ancient Sewers

 * "Even the guards seemed to know nothing about this part of the sewers. Or maybe they all just wanted to pretend it wasn't there."
 * "That same greenish substance, with its pestilent odor..."
 * "Mold everywhere... Spores floating in the fetid air... A perfectly welcoming ecosystem."
 * "One day, a pile of filth started growling. That part of the sewers was promptly blocked off."
 * This seems to be a reference to Conjunctivius.

Morass of the Banished

 * "A low lying part of the island where the leprous, diseased and quite often, poor, were sent to rot. The only refuge for survivors was in the trees."
 * "Taking to the trees may have kept the Banished safe from the ticks, but it didn't save them from the ravages of the Malaise."
 * "As the Malaise spread, the putrid stench of the fetid water and plagues of stringing creatures weren't the only things the surviving Banished had to deal with."

Black Bridge

 * "In the old days, the bridge linked the village to the prison and was only used on special occasions. In the old days..."
 * "Getting past the prison walls was a major achievement. Crossing the bridge was nothing short of a miracle."
 * "They say the prison warden was personally involved in guarding the bridge. So they say..."
 * "There are stories that curious fisherman used the river to avoid the bridge and get closer to the prison. Most presumed they drowned."

Insufferable Crypt

 * "The guards stored a lot of things in this old crypt. Weapons, provisions... and chains, just in case."
 * "Strange cries can be heard from the storehouse. Surely they're not human... No, no."
 * "The King decided to convert this old crypt into a storehouse. After all, there was still plenty of room in the cemetery at the time."
 * "Some of the guards tell of throwing bodies down there to feed her. Perhaps she just wanted to play?"

Nest

 * "No prayers, no words, not even deeds can rightfully honour our protectress; only sacrifice means true loss, and hence, true belief". The Sacred Barks, 20:1.
 * "Since time immemorial religious rituals have proven themselves to be extremely useful tools for eliminating one's enemies. This one also helps to keep the ticks at bay."
 * "Before dawn the Nest spills forth its wretched brood, ever hungry, hunting for their mother."

Stilt Village

 * "The village was first in line when the Malaise started to spread. At first they buried their dead. Before long, they were fighting them."
 * "It was a lovely village in the old days. Before everything there was intent on devouring you."
 * "Fishing was the main activity in this little hamlet, until the water started turning murky and dark."
 * "Before, it took several days for the fish to get that putrid smell."
 * A room with a woman who hung herself can be encountered. Her lasts words on a note are, "The Malaise won't get us. I'll protect you... I'll protect you." The bodies of two people with slit throats can be found in the bed nearby.

Slumbering Sanctuary

 * "The Stilt Village was built over a sanctuary, but it's hard to say whether that was an intentional choice by the original colonists."
 * "A mysterious energy runs through these walls, like blood through living veins."
 * "Some villagers claimed that the sanctuary was alive, that it could make the earth quake. Legends often tend towards the absurd."

Graveyard

 * "The local villagers came to pay their respects to their lost loved ones. The current population of the village has a different relationship with the graveyard."
 * "The only people buried in the graveyard are unknown villagers, far too common to deserve a place in the sepulcher."
 * "The dead have been buried in the Valley for generations. Now it seems there's something of a shortage of space."

Clock Tower

 * "The Time Keeper hasn't been seen for a long time. Or else very recently... Uh, wait a minute... When is now?"
 * "The first few hours in this tower can cause nausea, what with everything contracting and dilating at the same time."
 * "Some villagers claim to have seen the hands of the clock turning backward. Of course, those are just rumours..."
 * "A long time ago the Time Keeper obtained the King's permission to build this gigantic tower. No one knows the terms of the agreement."

Forgotten Sepulcher

 * "High-ranking dignitaries were embalmed in sarcophagi. After a somewhat brutal ceremony, the skulls of their delegation were used to decorate the walls of the chamber."
 * "Once reserved for high-ranking dignitaries, the sepulcher became a tortuous labyrinth, its reaches fading into obscurity and myth..."
 * "To get out alive, simply follow the light. No, not that one, the other... Yes, there, the... No, uh... Wait a minute, where are we?"

Easter eggs
Nathan Drake, the protagonist of the Uncharted series is found dead in a pit. He was looting sarcophagi but never managed to get back up because his rope was too short.

The head of Hollow Knight can be found, surrounded by other dead bugs, inside of a laboratory in the Ramparts biome.

Cavern

 * "The Cave is a strange place where ice and fire coexist. The Alchemist never found out how."
 * "Mining was the most thankless job on the island. Many died buried under rubble, suffocated by toxic vapor, or killed by strange creatures..."
 * "Precious crystals were unearthed from this cave on the King's orders. Nobody knows what they were used for."
 * "Longest time without incident: 45 seconds."

Clock Room

 * "An error of just a thousandth of a second in the calibration of the clock could have serious consequences."
 * "It's in this room that the Time K... No, it was in this room that... No, in this room the Time Keeper will... Hold on, where were we when?"
 * "The Time Keeper overlooks almost the whole island from here. The whole island, except the king's castle."

Guardian's Haven

 * "It is said that sobbing was sometimes heard coming from this lair. The Giant seemed to be a sensitive person..."
 * "The Giant didn't like the Hand of the King, and the Hand of the King didn't like the Giant. But they did agree on one point: nobody liked the Alchemist."
 * "The Giant came often to the bottom of the Cave to recharge. Nothing beats a good lava bath."

High Peak Castle
The Castle hides a number of lore rooms shining light upon the events that led to the downfall of the King and his court, as well as the whole Island.
 * "The royal guard stayed locked up safely behind the walls of High Peak Castle, thereby leading the island to its ruin."
 * "High Peak has fallen from its former glory... The last "banquet" held here served up human flesh."
 * "The island's high-ranking personalities came here to discuss important issues with the King. The quality of the visitors has changed a lot in recent times."
 * "The King allowed the Alchemist to move into a wing of the castle. That was around the time of the final retreat."

The Alchemist's Room
The blue room appears to have been a laboratory for the Alchemist, granted to him by the King as a last resort option. when he realized his ruthless methods were not working. Indeed, its shelves are full of various potions, vials and general scientific equipment akin to the various labs the Alchemist left all over the island. In the center of this room, where the Beheaded fights an Elite Slasher, endless rows of incubators can be seen, filled with mutated bodies. They are the same as those found in the Alchemist's Clock Tower lab, in which he was immersing infected bodies in an experimental solution in hopes of finding a cure to the Malaise.

It is unclear whether the Slasher enemy was a result of the Alchemist's experiments or if it is just another Malaise-infected character, but the fact that it is the Alchemist's Room boss suggests it could be the case.

The Human-Plant Room
The green room is host to a variety of plant-like structures, and its walls, floors and ceiling have been colonized by vines. In the center of this room, the Beheaded fights an Elite Thorny in front of a hybrid human-plant character who seemingly broke out of its incubator. This hybrid is the result of crossbreeding experiments by the Alchemist, in which he tried to administer plant extracts to a human "volunteer".

While the Alchemist reports that the experiment was a failure and that the subject did not survive, the fact that the incubator is broken and that the room has been invaded by plants suggest the hybrid did not actually die, and wreaked havoc in this part of the Castle.

It is unclear whether the Thorny enemy was a result of the Alchemist's experiments or if it is just another Malaise-infected character, but the fact that we fight it in this room and that the spikes on its back resemble the thorns of a rose (from which the hybrid seems to have sprouted) suggest it could be the case.

The Torture Room
The red room appears to have been a torture chamber, as evidenced by the various torture instruments scattered on the floor and hanging from the ceiling. In the center of this room, the Beheaded fights two Elite Dark Trackers in a pool of blood flowing from a fountain, with what appears to be dismembered bodies and skeletons hanging from the ceiling.

There is currently no lore in the game explaining the purpose of this Torture Room. It is unclear if it was used before or after the Malaise outbreak and the Island's downfall.