Tips for Running Mystery

[Parvum]

If you're that player of mine who browses the playground, turn your butt around or you'll ruin the game for yourself.

I'm going to run a little adventure, and I want to try to do a murder mystery with the players trying to track down the killer. I've got a few backups if it turns out I suck at it or the players aren't really feeling it, but ideally I'd rather just get it right the first time and give my players an engaging mystery that they solve through sleuthing and clue gathering.

So I'm asking for tips on how to leave clues, handle red herrings properly, and give the PCs enough information to keep them interested and engaged without spoonfeeding them the bad guy's lair.

I've been thinking of the scenario for a while, so I've got a clear idea of the villains motivations and murder methods... honestly, it might be getting overly complicated at this point. I'm kind of hoping that this might make it easier to leave clues? For most of the murders I've even got details of how the actual murder went, who saw what (in case the bodies are recovered for Speak with Dead) and the like. But I'm not sure how to organize clues, deal with what the players might think to search for, and generally handle something so player-driven.

That's the gist of it. Any general tips on clue creating are appreciated, but if anyone wants to offer context-specific help I'll put some details on the adventure below. The setting is high-magic and urban.
Quick summary:
Winona is a changeling (in the sense that her mother was a hag, not the eberron half-doppelganger) born to a loose coven of witches and hags. Her family was slaughtered by a band of adventurers when she was too young to remember, who took pity on the young girl and took her back to their home and placed her in an orphanage. Now Winona is a young woman, and the adventurers are mostly retired. The event is all but forgotten by everyone except for Tiriaq, the only hag who escaped the massacre with her life. She plans to resurrect the coven she once had, and she intends to do it with the only surviving member of her family, Winona. Enchanting her with druid magic and a silvered tongue, Tiriaq tells Winona about her past and convinces her that the Crusaders that killed her family are still coming for her, that they will slaughter Winona, Tiriaq, and every orphan that Winona has grown to care about simply for having sheltered her. She plans convince Winona to personally kill every member of the adventuring band that slaughtered her family, manipulating those around her to harden Winona to the act of murder and isolate her from everyone but Tiriaq. The final victim, kind Father Bernardo who sheltered and cared for Winona for most of her life, will be the sacrifice in a ritual to harness Winona's anguish, confusion and rage to transform her fully into an Annis Hag, a hulking magical brute bitter and hateful to all but Tiriaq.

There are eight victims, with three already murdered at the start of the adventure. The murders start a few months apart, getting closer and closer together. They speed up if it becomes clear anyone is on the bad guys' tail.
Proctor Chance, orc scholar.
Mercutio Deyes, retired veteran.
Maria Vasquez, homebody.
Brother Hiram, drunken preacher.
Julio, a fat fallen paladin.
Vica Aguerra, active crusader.
Jefe Gutierrez, nihilistic scoundrel.
Father Bernardo, owner of Sun Chapel Shelter, Winona’s orphanage.


Brief timeline without player intervention:
Proctor Chance is killed somewhat messily, baddies lay low for three months. Tuparnaaq picks up a hobby of hunting poor drifters in the slums, kills one. Deyes is killed, but Tiriaq has to recover the body from law enforcement when the pair forget to clean up. Maria is killed two months later, during those two months Tuparnaaq kills three more drifters. It is only one month later that Hiram is killed, two more weeks until Julio is targeted. Within the week Vica is led to Tuparnaaq’s lair and killed by the hazards there, where Tiriaq reanimates her as a slave and makes Vica attack the orphanage and kill Winona’s friends. Winona kills Vica with her own two hands, and demands the second last target from Tiriaq. She kills Jefe without shedding her skin and leaves the orphanage to live with Tiriaq. Tiriaq uses her as leverage to convince Father Bernardo to come to the lair, assuring Winona that the kind man she knew will surely be coming to kill her now that she has murdered all of his friends. She knocks Bernardo unconscious and claims he has a ward that protects him from full blooded hags, asking Winona to finish the deed. Unbeknownst to Winona, she has started a ritual that will be finished when Bernardo is sacrificed. Once completed, the ritual transforms Winona fully into an Annis Hag, and the confusion and feelings of betrayal makes Winona hateful and only willing to trust Tiriaq.

Tools of the Trade:
Winona has grown into a talented healer under Father Bernardo, but Tiriaq has taught her to turn that same magic towards destructive ends. In addition, her hag heritage manifests as claws that she trims each morning but have already grown to deadly sharpness by night.
Tiriaq has given her three gifts to help with the murders. The first is a fungus leshy named Tuparnaaq, a nature spirit given life that manifests as an assembly of plants in a tiny, studio ghibli-esque body. Tuparnaaq doubles as a magical moment that endears Tiriaq to Winona as well as an agent of Tiriaq that is almost always at Winona's side.
The second is a magic broom, which both allows her to make a quick getaway and keep the halls of the orphanage tidy.
The third gift is a ritual that lets Winona shed her skin, transferring her consciousness to it and allowing it to act on her behalf. It is able to squeeze through tiny spaces Winona could not and gives her other abilities of motion. It's primary purpose, however, is to distance Winona from the murders so she more readily takes a life. Though it is her mind, she (and her accomplices) refer to the skin construct as Quillac, Winona's birth name.
In addition, Tuparnaaq acquires a Cap of Human Guise after the first murder, a fairly common item that can disguise a small humanoid as a human child. He rarely removes it. He has a magic pistol that can track targets it wounds, as well as a dragon pistol (shotgun pistol) loaded with alchemical cartridges filled with his own vision-blurring spores.

The murders:
Winona and Tuparnaaq have settled into a routine for their murders. Tiriaq identifies the target and passes their address on to Tuparnaaq. He stakes out the house (disguised as an urchin) and begins to sneak in. Taking the shape of a large patch of mould, he tries to stay out of sight as he creeps into the house over the course of hours or days. Once inside, he examines the victim's house and routine for weaknesses. The process is slow and careful, and he can ultimately take several days before calling Quillac. When he feels the time is right and the victim is vulnerable, he finds an entry point for Quillac (ideally by cracking a window) and contacts Winona with a Sending Stone.
When Winona gets the call, she sheds her skin when the city goes dark, leaving her unconscious body under covers on her bed. Quillac then flies within a city block of the victim, walking and levitating the rest of the way. She is disguised, appearing as the next victim to be killed (after her current victim). She enters the house through the aperture and meets with Tuparnaaq. She then tries to tear the victim’s throat out with her claws while he supervises, Tuparnaaq intervening only if she cannot kill them instantly.
Once the victim is dead, they are stuffed into Tuparnaaq's Bag of Holding to be brought back to his lair, stuffed, and mounted. He also takes any firearms and any obviously magical items for himself.
Quillac leaves as soon as possible, waiting by her broom for Tuparnaaq to catch up. She then returns both of them to the orphanage.

Specific murders:
The murders haven’t all gone smoothly, even before the PCs start to intervene. In order of most recent killing:

Brother Hiram was waiting for his killers to arrive, refusing to sleep in his bed and pacing anxiously with a rifle in hand. All the windows in his house were boarded up along with his fireplace, and the doors were all barred from the inside. Eventually the sleepless nights got to him, and he nodded off while sitting in a chair with his back to the wall, watching the door. After days of posing as part of Hiram’s squalid home, Tuparnaaq finds a gap in the fireplace large enough for Quillac to squeeze through. Once she arrives, she rips out Hiram’s throat from the front, who wakes up and stays conscious long enough to squeeze the trigger of his rifle once, the bullet passing through Quillac as though through fabric. Once Hiram is dead he is loaded into Tuparnaaq’s bag and the pair of them pry off the boards over the fireplace so Tuparnaaq can fit through and Quillac can levitate them both away.
Unbeknownst to either of them, Tuparnaaq wasn’t the only one spying there. The next victim, Julio, has placed spies on most of his old crusader companions on the off chance that one of them committed the murders. There is a halfling spy who managed to see the murder, which looked to be the man who hired him (naked and eyeless) ripping out Hiram’s throat with the help of a small child and not even flinching after being shot in the stomach. Terrified, he hid until authorities found him and took him in for questioning, though he has refused to answer for fear of Julio’s retribution.

Maria was the simplest kill. Put at ease by Tiriaq in disguise (convincing her that all Maria’s troubles were behind her), she was sleeping when it happened but woke up in time to see Quillac, wearing Hiram’s face. The two murderers left with Maria’s body and were gone without a sound. Maria had the service of a maid who found the body next morning. Though it escaped her notice in light of the murder, the large patch of mould she had been fighting with for the past two days had completely vanished.

Mercutio Deyes’ murder was quick and efficient, he did not even wake up when attacked. However, the novice killers forgot to take the body with them. It was already in the hands of law enforcement before they could retrieve it, forcing Tiriaq to personally see to acquiring the corpse with forgery and deception before the other crusaders found out. She posed as a grieving relative, paying top dollar for quality forged documents and requesting that the body be released to her custody for imminent burial. The actual relative she was posing as was never made aware of this transaction.

The very first murder was the messiest. While Tuparnaaq’s infiltration went smoothly, Proctor woke up when Quillac entered his home gracelessly. Though she appeared to be Deyes, Proctor was not fooled for long and tried to incapacitate Quillac. She was unable to overpower him, and a frightened Tuparnaaq grabbed the nearest weapon- a magic pistol on display -and shot Proctor to death (this act started his interest in hunting humanoids). The murder was so loud and messy that Tiriaq intervened directly, entering the home to help stuff the body away and give Quillac and Tuparnaaq their flying broom to escape quickly. She herself left using Tree Stride in Proctor’s personal garden.

[Douche]

That guys name sounds a lot like Tupac

[Surpriser]

Mandatory reading for any mystery adventure: The Three Clue Rule (http://thealexandrian.net/wordpress/1118/roleplaying-games/three-clue-rule)

In summary: For every single conclusion you want the PCs to make, include at least three clues.
Also: You can never be too obvious, you can rely on the PCs to misinterpret what they find and create red herrings for themselves!

To sum up your plotline: A hag manipulates an orphan to kill a series of people from their past.
So, some conclusions that your PCs will have to make (in approximate order):

The victims are connected in some way (i.e. at least the first few were in the same adventuring party). This should be pretty obvious and come up as soon as possible, as it gives you the chance to introduce most of the major NPCs. If the PCs do not figure it out from your clues, have one of the surviving members seek them out, assuming that they publicly investigate the murders.
The killer was disguised as the next to-be-victim. Be careful with that as clever PCs could use that to derail your plot simply by kidnapping the intended victim, thus ruining Tiriaq's and Winona's plan. Consider changing that to some other disguise that makes it harder to predict the next victim, at least once it becomes known that the PCs are investigating.
The bodies of the victims were taken away, including smuggling Mercutio away from law enforcement by someone disguised as a relative.
There are at least two murderers, with supernatural abilities. The PCs should be able to get a rough idea of what these abilities are (e.g. nature-themed magic, shapechanging, broomsticks, ...). From this, and from interrogating the surviving party members, the PCs should be able to learn that the adventurers smoked out a coven of hags a few years ago and the murders could be connected to that.
One of the murderers, some kind of nature/plant spirit, also killed a few homeless people. This should lead to the discovery of Tuparnaaq's lair and possibly lead to the orphanage (I guess the lair would be hidden somewhere there to allow Tuparnaaq to remain near Winona at all times).


At this point, the PCs should know that the members of an adventuring party have been murdered in revenge for their killing of a coven of hags, probably by a survivor. They should also have found a connection with the orphanage, if only via Tuparnaaq.
Consider staging the attack on the orphanage at the same time the PCs find out about it. That way, they can get there and find Winona and Father Bernando missing and track them by the clues left on scene to Tiriaq's lair in order to find out about and prevent the ritual.

[Darth Ultron]

By default, D&D does not work good for murder mysteries. And first you really need to make sure your players want to do a murder mystery. The PC have tons and tons and tons of pure combat abilities and only a handful of non combat ones as D&D is a combat adventure game. A bunch of all combat adventures is a poor fit for a skilled detective.

When making clues, make sure to make them easy. Really, just watch any crime TV show for the level of clues.

And keep in mind that the best murder mystery type stories need a ton of unbelievable things to happen right in front of the characters(again, see any crime TV show). No one in a murder mystery type plot can act with even a penny of common sense, or they will never be caught.

[Parvum]

Mandatory reading for any mystery adventure: The Three Clue Rule (http://thealexandrian.net/wordpress/1118/roleplaying-games/three-clue-rule)

In summary: For every single conclusion you want the PCs to make, include at least three clues.
Also: You can never be too obvious, you can rely on the PCs to misinterpret what they find and create red herrings for themselves!

To sum up your plotline: A hag manipulates an orphan to kill a series of people from their past.
So, some conclusions that your PCs will have to make (in approximate order):

The victims are connected in some way (i.e. at least the first few were in the same adventuring party). This should be pretty obvious and come up as soon as possible, as it gives you the chance to introduce most of the major NPCs. If the PCs do not figure it out from your clues, have one of the surviving members seek them out, assuming that they publicly investigate the murders.
The killer was disguised as the next to-be-victim. Be careful with that as clever PCs could use that to derail your plot simply by kidnapping the intended victim, thus ruining Tiriaq's and Winona's plan. Consider changing that to some other disguise that makes it harder to predict the next victim, at least once it becomes known that the PCs are investigating.
The bodies of the victims were taken away, including smuggling Mercutio away from law enforcement by someone disguised as a relative.
There are at least two murderers, with supernatural abilities. The PCs should be able to get a rough idea of what these abilities are (e.g. nature-themed magic, shapechanging, broomsticks, ...). From this, and from interrogating the surviving party members, the PCs should be able to learn that the adventurers smoked out a coven of hags a few years ago and the murders could be connected to that.
One of the murderers, some kind of nature/plant spirit, also killed a few homeless people. This should lead to the discovery of Tuparnaaq's lair and possibly lead to the orphanage (I guess the lair would be hidden somewhere there to allow Tuparnaaq to remain near Winona at all times).


Thank you this is just what I needed! So I should have a list of potential clues for each of these conclusions, at least three each but the more the merrier. So obviously there will be clues at the murder scene, should other clues just go where different clues lead? Should I prepare clues in generic locations, like a local guard station, or stick to adventure-centric locales like murder scenes and bad guy homes?

I did figure that the PCs would try to go to upcoming victims, and I've got interactions for them. I mean, once they figure out that everyone's part of the same team they'll be able to guess the next victim with a one in four chance of being right. And if they do blockade one, there's three more. But that might feel cheap if the players are proud of themselves for figuring out who the next victim is supposed to be and the baddies just gank someone not under lock and key. But anyways I am hoping it moves them in the right direction, towards the future victims who can fill them in on what connects each of them. Once the players already know the victims are connected (and the baddies know someone is watching them) the disguise can change to something more generic. One of the PCs, probably.

[Surpriser]

I really recommend reading through the article I linked above.
It contains a neat description not only of the Three-Clue-Rule itself but also how to use it to build the structure of a mystery adventure using it.

I already tried to structure my list in a way such that the informations build upon one another.
For example, take the conclusion "These murders are connected". Assuming the PCs start their investigations with Brother Hiram, these are suggestions on clues to place:

Hiram has adventuring memorabilia lying around, including pictures of and letters from his old comrades. Some of the letters could include the killing of the others ("Did you hear what happened to Maria?"). The fact that he was prepared and waiting for the killer(s) must have originated somewhere after all.
Servants or passers-by remember "that old adventurer group", mentioning things like "Another one killed, would you believe it! And so close to each other, makes you wonder..."
Examining the crime scenes shows traces that point to the same killer (footprints, claw marks, magical auras, whatever). Speak with dead could come in handy here too (and also for most of the other conclusions - in fact, so much so that most of the victims should not have much useful to say unless asked very specific questions)
Last but not least, if the PCs still manage to miss or misinterpret these clues (entirely possible), one of the surviving party members could approach them and straight up tell them: "This is the fourth of us who was killed, someone is targetting all of us"


Now most of these clues are present in a single location - which makes sense, since there is only a single location known to the PCs at the beginning. As they uncover more information, you can place clues at a number of different locations (the crime scenes, the guard house, the orphanage, with any NPC, among the thugs hired by Tiriaq to "inconvenience" those pesky meddlers ,...)
Just remember that each of these locations must have at least three clues itself leading there (or, alternatively, someone explicitely telling the PCs: "Go there!")

[TheYell]

Whos in your party? A rogue would network villains while a paladin wouldnt go near the underworld. A wizard might try scrying rather than interrogating. Who are your sleuths and what do you assume will be their preferred method of invetigating? They will probably surprise you but at least you can be prepared.

You might be prepared to give them the solution if they can't solve it. Perhaps an accomplice refuses to go any further and confesses. Or a lawful evil sheriff identifies the culprit but marks him as "Escaped the jurisdiction" and blames the party for interfering. Then the party can have the fun of wrapping up the bad guy even if they missed the clues.

[Parvum]

Whos in your party?
Dunno yet. First session is character creation since a few people are too busy to make characters outside game time. Similar reason it took me a few days to get back to this.

I went and tried to pick apart all the revelations players need to keep the game moving. I split all the "Bad guy is X and has lair here" into "Bad guy is X" and "Their lair is here," save for Winona since her 'lair' will be spoonfed to the players on Revelation #1. I've got... well, I've got a long list. I'm just hoping the whole thing isn't too overcomplicated. Anyways I've got at least three clues for everything and most revelations have a Wall clue for if the players hit a wall and have no idea where to go. I'd like to be 100% objective but that's impossible since I made these scenarios in the first place, so I don't know if any of the clues make no sense outside my head.

Revelations and Clues:

The victims were all connected to the same retired adventuring group, the Crusaders Radiant.

Quillac is usually disguised as the next member to be killed (until the PCs figure out this clue/she figures out the PCs, after which she is disguised as one of the PCs to conceal her identity)
The pile of neglected mail in Hiram’s home has multiple letters from Maria, Vica, and Bernardo asking after his health and offering their concern. Several letters mention other crusaders.
Hiram has a small shrine to the god he falteringly worships, the only tidy spot in his home. The centerpiece is his old holy symbol which bears the generic crest of the Sun Chapel as well as the unique symbol of the Crusaders Radiant.
Maria has a single maid who cleans her home from time to time, and who reported Maria missing about a week after Maria’s murder. The maid knows that Proctor, Mercutio, and Bernardo would frequently visit Maria’s home. She also remembers occasional visits from Vica and a single threatening encounter with Julio, of whom she was once a fan.
Both Proctor and Mercutio have matching portraits in their homes of the pair of them posing dramatically. Proctor has portraits of the other Crusaders, though Julio only appears in a group portrait and even then his face is obscured by a potted plant.
Julio’s talking portrait in his home will go on at length about how he often saved the lives of the Crusaders Radiant, though it never mentions anyone by name except for Julio (several times)
Wall: Vica is pursuing the murders as well, and if the players do not make significant progress she catches up to them and tells them that all the victims are members of her old party.


There are at least two murderers using Non magic to kill

Each crime scene has two pairs of footprints, easily found. One set is always the same, a humanoid two legged gait with spongy or amorphous feet. The other set is consistently very faint, and always appears to be a different set of humanoid feet. Intelligent PCs can determine the less humanoid footprints come from a small creature, and the other set belong to a medium creature that somehow weighs even less than the first. PCs that can track the prints find they frequently vanish and reappear on rooftops, either by flight or by superhuman climbing, and that all tracks vanish about a city block from the scene.
Maria’s maid noticed a patch of mould in Maria’s home that she could not get rid of. More strangely, it clearly teleported away when she returned to clean it, only to appear elsewhere in the home. She describes it as a patch of weeping rot and lichen the size of a small child. She did not check for it after Maria vanished, but it is no longer there if anyone searches the home.
In Julio’s home, Tuparnaaq was cornered by his advanced security system of clockwork constructs while trying to contact Winona, and dropped his Sending Stone in the mansion halls. The patrols are too regular for him to search for it.
Mercutio’s body is gone, but his Speak with Dead transcript reveals that he saw “Someone small, pointing something at me.” When asked what he heard, he said, “The person in front of me spoke. Someone else spoke. I did not understand.” When asked to repeat what they said, Mercutio’s body offered gibberish. A clever PC can determine that the gibberish is supposed to be Nonnish, which Mercutio didn’t speak.
Vica’s own leshy, Awamp, enjoys speaking to every plant they can. When Vica brought them to the murder scenes, the plants all commented that another leshy had been asking them questions about the animals that lived inside those houses.
If any of the players see Quillac and describe her to any of the Crusaders, they shakily explain that they have seen that magic used before by a coven of witches that used constructs made of hollow skin to attack them. The skin creatures were just as strong as a solid creature, impossible to crush or skewer, and could levitate.


The murders are revenge for the slaughter of a hag coven in the Crusader’s past

The Crusaders recognize Quillac’s Skinsend ritual from the witch coven they killed in their past, the only time they had ever seen that magic.
Speak with Dead on Proctor or Hiram, who both saw their murderers clearly, reveals that they immediately recognized the Skinsend construct and leshy and concluded that the coven they slaughtered had come to take revenge.
The walls in Julio’s private sanctum are smeared in mad scribbling, “WHO DID WE WRONG?” or “THE PAST HAS COME FOR US SINNERS” and other fearful proclamations claiming that someone from his past is coming for him. If they can ask Julio directly, he believes that one of the many people the Crusaders zealously murdered for the greater good is coming to take revenge, but he doesn’t know which one.
Bernardo, who is closest to Winona, remembers the coven clearly. He is hesitant to put Winona in danger by outing her. If the players convince him to share information, he tells them about the coven on the one condition that they promise to protect Winona from not just the murderer, but the Crusaders as well.
Wall: A mole in Tiriaq’s organization sends Proctor and other undead servants to attack the PCs. The attack is cover so that her betrayal isn’t recognized- the purpose is to send Proctor with a message: “A coven is not so easily destroyed. Our sisters will always return to the fold, and those who would hurt us will wither and die!” Once the attackers are dealt with, the PCs will also have Proctor’s body.


One of the murderers is killing vagrants in the Warren disguised as a human child.

If the players intervene at any murder (most likely Julio) they may see Tuparnaaq for themselves or even catch him.
Seeking out urchin children that match Tuparnaaq’s description is impossible to miss. Floods of them enter The Urchin Cap, an exclusive bar where the PCs can learn about the popular Cap of Human Guise. The members are aware that a killer stalks the streets with one such hat.
Proctor’s home has an empty display case near the signs of struggle. It was sized to fit a pistol and an engraving on the base reads, “The Warrens owe you one, but consider us even. -J.” investigating the Warrens for J leads to the wall clue.
There are bullets and bullet holes in both Proctor and Hiram’s homes. Clever PCs can determine telltale signs of magic in the property damage. Investigating magical firearms leads to the wall clue.
Mercutio and Hiram’s homes had gun cabinets that were looted of firearms and ammunition. Nothing else was taken from either crime scene.
Wall: If the players are stuck, they are sought out by one of two groups. If the players follow gun related clues, they find these groups themselves. Proctor’s gun, the one Tuparnaaq now uses to kill homeless drifters, was an unlicensed firearm made and gifted by Scarpering Jen. The local gunsmith is one infraction from being shut down, which will happen if Proctor’s gun is discovered. Her rival wants this to happen. Either group is well aware of the small urchin child killing people in the Warrens, though they haven’t been able to track them down. If they meet the PCs, they describe what is known of the child and offer a reward for the weapon. Jen can also tell the players about the popular ratfolk item, the Cap of Human Guise.


The bodies that have been taken are in the sewer underneath an orphanage, in the lair of one of the murderers

If the players recovered Tuparnaaq’s sending stone and use it immediately, a confused Winona asks them to “Meet me by the entrance to your sewer.” If they wait, Tuparnaaq directly instructs them to his lair for an ambush.
Players investigating Non magic hear about an illegal grove of plants in the sewers, clearly Non magic.
Asking after a well armed urchin gets the players an account of a man chasing such a child halfway across the city and into the sewer. Streetwise PCs can track the eyewitness reports to the right sewer entrance, otherwise they learn that the man was an instructor at Little Tadpole Swimming school. An unknowing dupe for Tiriaq’s operation, he saw Tuparnaaq trying to sneak into her lair through the school. He chased the leshy all the way to the sewers and lost him in Tuparnaaq’s fungal forest. He gladly leads the PCs there.
The orphans on the Sun Chapel Shelter have made a new rhyme: “Do you know the mushroom man, the mushroom man, the mushroom man? Do you know the mushroom man who lives under the stairs?” The children know that Tuparnaaq is a secret and won't talk about him with adults.
The basement on the Shelter is boarded off for a deadly Russet Mold infestation. Players that investigate anyways can find a pair of breathing masks hidden under the stairs. There is a service hatch to the sewers buried underneath the mold.
Wall: Tuparnaaq takes on one of the PCs as his personal quarry. If he is captured, he tries to lure the PCs to his lair and hopes the fungi kill them. If he is killed, his possessions include a note from Ing and Lake, two orphans that help him stuff bodies, that explicitly mentions their activities. If Tuparnaaq succeeds in killing or knocking out a PC, he tries to bring the body back to his lair and can be easily tracked or followed.


One of the orphans, Winona, has been using the same hag magic used to kill the victims

Father Bernardo came to check on Winona one night and found her body stripped of skin. She was fine the next morning and Bernardo has since dismissed this as a troubling nightmare
The orphans at the shelter know that Winona and Tuparnaaq are best friends. If the PCs confront Ing and Lake in the sewer lair, they will bargain this information for their lives.
The bodies in Tuparnaaq’s gallery of horror are all in excellent condition for Speak with Dead (but too hollow for Raise Dead). Hiram’s body (as well as any freshly murdered Crusaders) know that it was a hag skin construct that killed them.
Winona's broom has an engraving on it in Nonnish: From Auntie. There is an addition in Druidic, a pun about witches.
There is a ritual circle underneath the rug in Winona’s small room. It is covered in symbols that call to mind a figure screaming in anguish as their flesh flies from their bones.
All the crusaders know about Winona’s origin save for Vica. Father Bernardo hides her past for fear she will be targeted, but persuasive PCs can get the truth out of him. Jefe will speak freely if the PCs ask or if they mention hag magic, suggesting they ask Winona if she remembers anything. If Julio is reminded of the connection, he assumes that the hags are seeking revenge for their slaughter and that Winona is another potential target.
Wall: The Shelter is attacked. Winona defends it using clear hag magic and then flees to Tuparnaaq’s lair if he hasn't been uncovered, otherwise she flees to Tiriaq’s lair on the magic broom. If the PCs never meet Vica or allow her to pursue the case on her own, the attacker is Vica’s zombie. If the PCs never speak to Julio or rile up his paranoid delusions, he attacks the orphanage. Otherwise the attackers are thugs sent by Tiriaq claiming to represent the Crusaders Radiant.


There is a more powerful hag that has been manipulating pawns to kill her targets

Mercutio’s body was claimed by a woman appearing as his relative. The relative in question had no knowledge of this, and close examination of the paperwork reveals it to be high quality forgeries.
Awamp’s blathering mentions that the trees near Proctor’s home were used to transport a creature using Tree Stride. The trees know that only a single creature walked through them recently, nothing more.
Winona keeps a diary, and in it she describes how wonderful it was to meet her Aunt Tiriaq. The diary describes wondrous nature magic and spells, along with Tuparnaaq’s creation, and abruptly stops after an entry that says Tiriaq, “Promised to show me a magic spell that will open me up to the world and show me things I never thought possible! And she says there is something else really important she has to tell me.” Afterwards the entries cease, save for a tally numbering 4 (more if other victims have been killed). The diary is now kept in Tuparnaaq’s lair.
The orphans know that Tuparnaaq only showed up around half a year ago, and that Winona will only say he was a gift from someone special. If Winona is gone, they approach the PCs with this information.
Wall: An NPC finds Winona’s diary and brings it to the PCs.


The hag is sponsoring a burgeoning cult in Three Terrace Sanctuary, a seemingly peaceful organization in the residential district.

In Ing and Lake’s lab inside Tuparnaaq’s lair, there is a board of notes left between Lake and Tuparnaaq. Most of them have to do with dissection and taxidermy, but there is also a reminder that neither of them are to enter Three Terrace through the front entrance- Tuparnaaq adds that he was harshly scolded by “Aunt Tiriaq” and chased across the city by an instructor.
Winona has a flyer for Three Terrace in her room.
There is a flyer for Little Tadpole Swimming School in Winona’s diary. The school operates out of the same building as Three Terrace. The instructor that chased Tuparnaaq works there, paying rent to Tiriaq, and is worried about a student of his that’s gone missing after investigating deeper into Three Terrace.
The skeletons that serve Tiriaq are warped by a special substance she concocts, Waters of Maddening, that twists and strengthens them. Wildlife around the area of Three Terrace show mutations similar to the skeletons she uses to guard Tuparnaaq’s lair or hinder the PCs.
If Winona has left, Tiriaq contacts Father Bernardo and uses her as bait to draw him in. If the PCs cannot track him, his secretary also knows where he was going, though she promised not to tell anyone.
Wall: The secretary gets cold feet and seeks out the PCs to tell them where Bernardo and Winona went even if the PCs lack persuasive skills.

[TheYell]

You've put a lot of work into making it sensible. Let us know how it's going. I hope the players choose useful builds for the mystery.