With much thanks from laine, Madz, and TopG from the FAITH Community Discord, they were able to data mine all used assets and audios for The Unholy Trinity. With this, I (Screamin' 'n Hollerin') organized all the assets and compared them to whether they appear in-game or not. Here's the collection, from Chapter I, II, Prologue, III, and Demon Siege.
Chapter I[]
Michael's Beta Audio[]
In an early development build that can be seen in the Goodies Folder, Michael originally did not have spoken lines when he appeared onscreen, instead making a distorted version of the Pokémon (Silver) Murkrow's cry.[1]
Unused Notes[]
Before The Unholy Trinity, there was three unique versions of Chapter I that varied on which website you downloaded the game from, Game Jolt, itch.io, or indie DB. The differences are relatively minimal and doesn't affect gameplay too much. The biggest difference is that it changes the note Michael drops after warding him off ten times.
For the GameJolt version, the note is about one of Cindy Martin's friends, Nancy, seeing a tall man in dark clothing during the Martin Twins' birthday party. The itch.io version has Cardinal Gifford instructing Father Garcia to release Michael back to his parents, and the indie DB version is a newspaper article released on the morning of Sept. 21st detailing how a Sterling local named Cherise saw a naked white man run on the side of Snake Meadow Hill Road on Sunday, Sept. 20th.
The Unholy Trinity uses the itch.io version because we get the note from Cardinal Gifford, meaning the other two notes are unused. Here they are:
“ | "NAKED WHITE MAN" SIGHTED ALONG STERLING ROAD
A Sterling resident called the police last night claiming they saw a "naked white man" cross the road in front of her while driving home the previous night. Cherise Wan, who owns a laundromat in Sterling, says she was driving on Snake Meadow Hill Road on Sunday night when she saw someone run out into the road in front of her car. "I saw the side of the road. I slowed down because I thought it could be a deer but it was this naked white man running across the road. The way he ran on all fours on the ground, he looked like a big white spider." When asked how she knew it wasn't an animal, Wan told reporters, "It couldn't have been a deer or dog or any kind of animal. I saw its face. It looked right at me and it was a human's face." |
” |
— Exclusive Note in the indie DB version of Chapter I
|
ㅤ
“ | I just got a phone call from Nancy about a man she saw at the twins' birthday party. She described him to me: a tall man wearing dark clothing. I honestly cannot figure out who that could be. What frightens me to death is that she said she saw him talking to one of the twins away from the rest of the party. It's a good thing Nancy is single and lonely. How did I not notice a total stranger hanging around at my sons' birthday party? The sheriff is going to come over tomorrow and ask about this man. This is too much for me to handle. I need Bob here, not in the Middle East. | ” |
— Exclusive Note in the Game Jolt version of Chapter I
|
"Winners Don't Use Drugs" Screen[]

In the standalone version of Chapter I, in the boot-up sequence there was an image that reads "WINNERS DON'T USE DRUGS", seen here. It is a replica of almost identical screens that appeared in arcade games in the 80s, during America's "war on drugs". For unknown reasons, it was removed from Unholy Trinity's boot-up sequence but still remains in the game's files.
Handlers[]
In the standalone version of Chapter I, the icon for the program would change occasionally to either Amy, Michael, or a Deer. These are unused since in The Unholy Trinity the icon stays the same, a red cross in a black background.
Title Screen[]

Before The Unholy Trinity, the basic title screen of FAITH was used in the standalone version. In the final, it was replaced with "FAITH Chapter I" in gold/yellow text.
Chapter II Prologue[]
Due to how short Chapter II's prologue is, there aren't a lot of unused assets in this one.
Cultist[]
Cultists were apparently supposed to appear in Prologue since they're in the folder for all the assets used in that game. However, they never appear. Their appearance is the same as we see in Ch I, II, and III.
Cultist Boss[]
Gary was also supposed to appear in Prologue, but he doesn't make an special appearance in this prologue unlike chapter 1.
John Sprites[]
The sprites seen in Ch I where John is split in half by Michael, ran over, and crawling to grab his crucifix in an ending are in this games files as well. It seems they were just assets dragged over to this game.
Michael Splat[]
The sprite seen in Ch I where Michael is run over by a truck was supposed to be in this game but, it's unused. It's likely that it is just a left-over asset from Ch I. But, considering how Prologue seemingly starts right after Ch I's "When Faith Endures" Ending, it could've been used as a way to connect the two games together.
"three days until profane sabbath" Title Screen[]

A title screen saying there's three days until the Profane Sabbath never appears in this game. This screen is slightly different than the final version of Ch III since in that game there's big text that tells you what date it is then how many days you have left until the Profane Sabbath.
Chapter II[]
A lot of the unused assets from Chapter II were just carryovers from Prologue.
"Winners Don't Use Drugs" Screen[]
A screen identical to the one found in Chapter I also existed in the standalone version of Chapter II.
Pelo[]

There's a crude drawing of Sr Pelo, an internet comedian and illustrator, in the files. There's one graffiti in the Candy Tunnels that say Pelo on the walls, so this was most likely unused due to how it would of been out of place in the game.
Old Father Garcia Design Cinematic[]
After unlocking a door in Malphas' House, cinematic plays where Miriam tries to grab John's face/neck but she disappears in pain when Father Garcia comes in to save the day. In the standalone version of Ch II, Garcia is a less detailed reskin of John, where he's gray instead of blue. In The Unholy Trinity, it's an outline of a more detailed version of Father Garcia that we see in Ch III, reminiscent of the gray figure in Ch I.

This scene is no longer in the files of The Unholy Trinity, which makes it unique since all the other standalone-exclusive assets are still in the files for Ch I and II.
Miriam Unused Distortion[]
During the fight against Miriam, she occasionally twitches. However, if John successfully performed all the conditions for the "Initiation" Ending, this sprite was used when she twitches instead. This doesn't appear in The Unholy Trinity, her poses stay the same regardless of what ending you get.

Carryovers[]
A lot of assets are unused since they only appear in Prologue. The only reason this section exists is that they're renamed from "CH2P" to "CH2". These include the Shadow Crawler, Chalice Demon, Corn Maze Demon, Red Eyes in the Scarecrow, Pile of Rubble, and so on.
Title Screen[]

Like prior, this title screen was used in the standalone release of Chapter II. The Unholy Trinity replaces it with "FAITH Chapter II" in silver.
Chapter III[]
With how lengthy Chapter III is, there's more unused assets here compared to the others.
Early Martin House 86'[]

This is an earlier version of the Martin House, where it has a smaller roof and house next to it. You would assume that this version would've been in Ch I since there's no reason for the design/layout of the house to change between games but here it is.
Martin Twins Room 86'[]
During the nightmares of the first exorcism, John can enter any room in the Martin House except Nate and Jason's room, saying "I can't remember anything further." But there's an 86' variant of the twin's room. It looks almost the same as the room we see in Ch I, but there's a grayscale applied to it, and it's lacking the twin's beds.

Pentagram 86'[]
This pentagram is the grayscale version of Amy's pentagram that she uses in Ch I. This could either be a carryover from Ch I or she was intended to attack John during the nightmare.

Bob Martin's "Scary" Sprite (move to character)[]
In a nightmare where John walks to the attic to confront Amy, you can see Cindy standing behind objects throughout the house and Bob trapped in a mirror in their bedroom. Due to how tall the mirror is, you cannot see his full face, only his bloody body. Here's the sprite in full:

Cindy Martin's "Creepy" Sprite (move to character)[]
In the same nightmare where we see Bob's "Scary" Sprite, we can spot Cindy hiding among furniture or mannequins. Because of this, we never see her sprite in full, so here it is:

"hey" Audio[]
This is a realistic sound of somebody knocking on a door. In the Chapter III Demo, this was originally a recording of someone whispering "Hey." into the microphone, and would play if the player decides to stand still for one minute after picking up the camera during the apartments section. In FAITH: The Unholy Trinity, the sound goes unused, as the "finders" audio will always play instead.
Super Miriam Alternate[]
In the files, there's a different variant of Super Miriam that has her body shaded gray. It's never used in the game; her brown body and ragged black cloth stays the same throughout the fight.
Super Miriam's Mock Projectile[]

This is just a plain ol' white skull that's used by Super Miriam. In the final, the skull is yellow and green.
Amy Cleansed[]

When Amy drifts down from the darkness after beating Super Miriam, she was supposed to display this sprite, but it's never used. It's tough to say if it is, though, because it's a complete black outline of Amy, which could have possibly been her shadow. The area we fight Super Miriam in is completely black, so there'd be no way to see this. But that's a stretch, I'm really not sure.
Basement Freak[]
This one's unique, it looks almost like Jeffrey, but its neck is broken and is slightly taller than Jeffrey. It's found within the same assets used for the bad ending version of John's House. It was likely an earlier version of the Centipede Demon's functions where it tries to hunt John after he grabs a key. In the Goodies Folder, there's a rough draft of what John's basement was supposed to look like. It's a bit smaller and more secluded than what we see in the final, making this creature a perfect fit.
Other Basement Freak[]
Almost the same design as the other freak except its broken neck is in a different angle. It's not the same freak because the filename has "other" in it, possibly indicating that these two were supposed to team up and try to kill John. Not too sure about that, though.
Ugly Demon[]
An unused demon found in the data files of FAITH: The Unholy Trinity. Interestingly, alongside the demon's idle animation, there are separate animations for the demon's body by itself, and the demon's red appendages apparently emerging from its body, according to sprite nicknaming. This implies that this particular demon was either meant to have its own introduction animation, or its size was meant to be a mechanic in its encounter, changing the area of its hitbox by extending its limbs to attempt to reach John.
Other Demon Sprites[]
These demon sprites were found in the sprite sheet for Faith: Chapter III. Although speculated to be in the game, they never made any appearances.
The Conjoined Demon could have somehow been related to the Martin twins, however it is impossible to know whether this was actually the case.
The Cult Priest is presumably a grey human male in clerical-like clothing. Just like other priests, he has his own crucifix, but it has a red and evil color instead of the typical gold, silver or bronze.
Garyland Cage Mockup[]

This is an early/beta version of a room in Garyland. In the final, there's two cultists sustained in cages, a table, and a statue of Magog in the center. This unused one is interesting, there's nobody in the cages, a blood trail from a cage, no Magog statue, a tool with appliances on it, a thrall on the wall, and there's two pillars that are seen previously near a statue of St. Death. This room also shows that the layout of Garyland was different, since in the final you enter the room from the bottom screen but in the early version you come in from either the left or from the bottom.
John's House Mockup[]
This is an early/beta version of John's house from outside. It's almost the same as the final, except that there are pebbles that lead you to his silver sedan.

Gary Pondering His Orb[]
This is a gag on the "Pondering Your Orb" meme but, with Gary and John in it. This image is also found in the Goodies Folder.

John aims at the UNSPEAKABLE[]
This one's also in the Goodies Folder; John points a Anti Tank Rifle at the UNSPEAKABLE.

Fun fact, Airdorf posted this same image but with Gary and Cultists in the background on his Twitter[2].
PT Lisa GIF[]
This one's a pixelated edition of Lisa shaking uncontrollably from the cancelled psychological horror game, PT. This gif is also found in the Goodies Folder.

Pelo[]
Like from Ch II, Pelo makes his return here. Nothing new, just a simple gag.
Morbius Death Screen[]
A gag on the "Morbius" meme, where it says "morbius" instead of "MORTIS". It's also found in the Goodies Folder.

Fun fact, there's no audio of John saying "Morbius" in the files of Ch III unlike in the Goodies Folder.
Demon Siege[]
This is a Shoot 'em up fan game for Faith the Unholy Trinity made by CrackedGhostGames on Gamejolt. This is automatically downloaded and placed in the goodies files when you download Faith.
Rare Death Screen[]
It's hard to say whether this is used or not since I've yet to seen gameplay footage of somebody getting this or through my own playthrough of it, hence why this is here. Instead of the normal death screen, John's body shows his bare skull. The body flashes black and white, but no example is here due to it's harsh flashing lights. There's also a red screen with a heart monitor that's supposed to accompany this.