As you complete the base game, at the very end it gently nudges you into digging deeper into the game files and discover that there's a lot more stuff with Estigma than you initially think.

I encourage you to try going through it yourself first, then come back to the guide to see what you may have missed (or if you're stuck). I will not be spoiler-tagging the majority of the guide, as it just makes it much harder to read.

Once you complete the last "regular" level of the game, the final stage is unlocked. It reads:

"T4m4sh112" can be interpreted as "Tamashii 2", which would be a sequel to Tamashii.
It is a 2019 game from the same developer.
The sequel isn't out yet (as of March 2022) but there's gonna be more to it here.
Tamashii 2 was re-branded as TEOCIDA and released in Dec 2021.

So before you play the level, this message is displayed:
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This is a motto of Alchemy that translates as "dissolve and coagulate":

Originally posted by https://www.synergyalchemy.com/solve-et-coagula:

“Solve et Coagula” means to dissolve and coagulate, to break a substance down to its basic elements before reforming it into something new. This could be analogous to the destruction of one’s ego before the realization of the true self, or the distillation of a substance down to the prima materia to make alchemical preparations in its purified state of the principles of alchemy.

These are also the words you see written on Baphomet's arms.
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So we got ourselves some "nice" occult / alchemy lore going. But don't worry. It gets worse.

The final level looks like this.

You need to pick the correct symbol for The Mind, The Body, and The Soul respectively.
The correct answer is right, left, top symbol in this order.

Your player character now transcends / shapeshifts into a human, slowly descending down.
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Then some disturbing imagery is shown to you. Here's a frame (the skeletons' heads are slightly animated in-game but otherwise it's pretty much static).
[Updated 16 May, 2022] these are most likely low-resolution frames from this video on the developer's Youtube channel.
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Then this. Typos are part of the aesthetic[img.itch.zone].
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And finally, this part.
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This message is displayed indefinitely and the game will immediately quit when you press ESC.

Go to your Steam library. Find Estigma. Right-click it, select Manage -> Browse local files.
You should see the game's data folder.
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We're gonna need page3.jpg and page4.jpg soon. For now let's look at the "secret folder".

There are three .rar archives here, all passworded. You'll need to use software such as 7Zip (or WinRar... I won't judge...) to open it.

If you can't be asked to install 7Zip (which is a good tool to have regardless) then you can use these zip repacks[www.dropbox.com]. I have extracted and then repacked the exact same content with the same passwords, except now it's in zip format so default Windows tools should open them easily. The only difference is that it kinda spoils the folder structure and file names (because unlike zip, rar and other formats can actually hide everything in the archive, while zip keeps the structure & filenames exposed) but honestly it's not very important.

So we were told we are granted access to additional intel. And there's an archive here literally named "Additional Intel". However, the code given to us (37 26 48 15) is not the password itself. We need to figure it out first.

Let's look at the contents of page3.jpg and page4.jpg in the game's base directory.
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We can combine the two pages into a single table.
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It is quite easy to deduce that our code 37 26 48 15 translates to the password SETH
However, it actually must be entered with lowercase letters: seth.

Open the archive, extract it, and we get... A whole bunch of new pages and a Unity game?!

Before we dive into the game, let's take a look at the three new pages we got.
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The last page clearly states that we need to use the password "<crescent><circledot>" to open Elemental.rar. The other two pages tell us how to figure out each of the two parts of the password. However, page5 obviously lacks data and page6 is burned up, so not much to do other than play the Unity game.

Double-click PLAY.exe to start it.
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Well, that's some main menu. The text is incomprehensible but we can press the button below to start the game.

And we get here.
Yup, it's a first-person horror that was already shipped with your Estigma download.
Well, this is... Deeply unsettling.

Here's an important disclaimer. This mini-game is very creepy, but be advised that there are absolutely no jumpscares anywhere in it. In fact, if you're like me and too scared to play games like this, know that there are no monsters to chase you here. Nothing will pop up from the dark when you least expect it. This is essentially an empty hallway with some classrooms and some unpleasant ambient sounds near the staircases. If you turn your volume down you can relax and play this safely. Games like this are scary due to fear of the unknown - you don't know what to expect next. Well expect nothing in this case - just explore the classrooms safely and exit. Nothing will appear suddenly. I hope it helps.

Here's a full video playthrough.
https://youtu.be/SIRqs26cQVI
Anyway. Points of interest include:
This is the answer to the crescent part of the our password. We'll get back to it soon.

This is simply the link to Tamashii[vikintor.itch.io], the developer's other game that we already mentioned earlier. The game is also on Steam.

And here are letters with colored backgrounds, which is exactly what we need for our circle-dot.

There are also some minor concept arts of... some games I think, but they're not particularly interesting. They are included in the video above. But for now it's all we can get from the game.

Here's all we've got on the crescendo-symbol part of the puzzle.
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Should be obvious that the answer is HELP. Or rather, since the game actually expect lowercase letters from us, it's help.

Here's page5 again, but we added the characters we found. We now obviously need to translate them into numbers. Not only the phone pad is there for a reason, but also we cannot use the previous table to reverse-translate letters into numbers (K = 28 etc) because the letter D isn't present in the table at all.

Anyway, let's use the dial pad numbers.
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The catch here is that you would think that the answer is 5+3-(2x9) = -10.
However, you need to ignore the operator precedence and just calculate it from left to right.
Kind of like (5+3-2)x9 = 54.

Finally, let's combine these two parts. Here's a reminder how.
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The final password is help54

Let's open Elemental.rar. It contains 1 image.

Yep, we're going back to the same game. Exactly like Elemental.jpg suggests, click on these three symbols in the left-to-right ("reading") order:
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And we're back to the classrooms. Except... It looks far worse this time.

Again, disclaimer: although this part is scarier and somewhat more intense than the original classroom, there are still no jumpscares in it. If you are still too scared, turn your volume down, try to relax and always keep in mind that nothing will jump at you. There are no enemies in this game. You're safe.

Here's a full video playthrough.
https://youtu.be/tVor_DpLl64
There's nothing really to explore or discover this time.
Almost everything is blocked off except this lit up corridor.
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It's long, completely dark, and there is a deeply unsettling moaning all the way through.
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We find a lit up classroom at the end of it.
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Unfortunately, we immediately fall through the floor upon entering.
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We are now walking... Here.
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Take a guess what's at the end of the path.
Yup, our final password. Nothing more to do in this game, so press ESC to quit.

The password is given to us, but again as usual it's actually expected to be lowercase so you need to input "aton"

Here's the overview of archive content.
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So here we have:

• A small bonus game
  
• Soundtrack of Enigma
  
• A few extra pages!
  
• And mostly concept art, screenshots, animations etc from the upcoming Tamashii 2.

I'm not going to upload every single piece of Tamashii2-related art but I threw together a general glimpse at the content.

Note that Tamashii 2 has been re-branded as TEOCIDA and released in Dec 2021.
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As for the extras pages.
thanks.jpg
Spoilers: it's not quite over just yet :)
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page1.jpg
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page2.jpg
We'll get to this one later.

Here's Excerto do manifesto.jpg ("Excerpt from the manifest").
It's in Portugese, so I google-translated and recreated it in English.

Estigma soundtrack is self-explanatory, so time to look at the small bonus game.

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Luna Chicha's Arcade is a fairly primitive game in which a little girl is dodging various objects while apparently performing a demon-summoning ritual.
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The game has four difficulty settings, and you need to get enough points in a given difficulty to unlock the subsequent one.
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The game isn't infinite though, and soon after you hit your score target the cutesy-looking devil comes out and dances with you.
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Here's a full video playthrough of the final difficulty, Nightmare.
The ending in it is the same as in other difficulties.
https://youtu.be/-HjvNaxpyv8
I didn't manage to find anything else in the game. I've tried to do a no-damage run but it didn't seem to matter. I don't think there's much left to discover in this game though.

Let's get back to page2.jpg.
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So this is obviously some ciphertext. How do we decode it?
Well, let's start by looking back at these pictures again.
We already know how to decipher 4 of the letters - H, E, L, P.
Importantly, one of them is a vowel: this one is E.

Now let's look at the cipher text again. What's interesting is that we can see several letters E as separate standalone words, one letter long each. Clearly, English doesn't have "e" as a word.
But you know what does? Portuguese. Not only we already had a different document in Portuguese, but the developer himself is also from Brazil.
This document is written in Portuguese.

Regardless, working with these pictograms is a nightmare.

We can assume that the full-black square is a period, given its locations in the text.

With that, there is a total of 24 different symbols in this text.

We already know 4 of them. I enumerated all the other ones with numbers from 01 to 20 and got the table on the left.

It is now possible to re-encode the original ciphertext as this:

It's still a mess, but it's plain text that lets us work with it nicely.

For starters, let's split this text up word-by-word, then sort the list of words and keep the unique words only. This is the result[pastebin.com].

Now. Remember the main menu of the classroom game?
Let's think about the button here. As it essentially works as "new game" button and consists of 5 characters, it would be natural to assume it's something like "BEGIN" or "START". Could be in Portuguese too, though the languages are fairly similar. Regardless, the important part is that not only 1st and 4th characters are the same here, they are in fact letter E that we already know!
So the button spells E**E*. Initially I thought it could be "EXPEL" (because classrooms?) but we also know what letter L looks like in this ciphertext and it's not that.
In the end, it is safe to assume that the button spells "ENTER" (spoiler: yes, it does). This gives us three additional letters from get-go: N, T, R.

We can now find-and-replace 05 -> N, 15 -> T, 14 -> R in our list of words.

At this point we simply iterate over the list of words again and again to find something that makes sense (especially to someone like me who speaks no Portuguese).

• I found the word || r e p r e 11 e n t e 04 ||. While I don't know how word endings work in Portuguese, it's safe to assume that 11 is S.
  
• Word || t r 06 t 06 r || uses the same vowel twice. I tried to google-translate tritir, trotor etc but only tratar is a valid Portuguese word, so 06 is A.
  
• Words || 08 n t e r p r e t a 07 01 e s || 08 n s t a n 07 08 a || 08 n t e r 08 01 r 12 || all sound sorta like || interpretations || instance || interior || in English so it's very likely that 08 is I.
  
• Looking at || e 13 p e r i e n t a r ||, I just intentionally skip one unknown letter and Google Translate it (as eperientar). It immediately suggest experientar, so 13 is X.

This gets easier and easier from here on so I'll skip the rest of the details.
Instead, behold - the final cipher table.
Note that this text does not contain letters Y and W (we get to find them later). We also never see letter K at all, but going off the patterns I think you'd agree it likely would look like that.

Time to finally decipher stuff!
page2.jpg
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Classroom game menu
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itch.io game page[vikintor.itch.io] also contains this:
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And before I forget, page1.jpg contains a higher resolution logo of the "program":
This is a quote from Emerald Tablet[en.wikipedia.org], an ancient cryptic text that lies in foundation of alchemy. Unfortunately I'm much more of an IT engineer than a historian or esotericist so it's up to you guys to interpret all of the lore here.

Thankfully there appears to be little to no protection against decompiling the classroom game so I took a dive into its data. I used uTinyRipper for this.

First, I found page8!
The internal texture name for the page with ATOM password (at the very end of corrupted classroom) is page9, so this puts page8 between the two passwords. Searching interally for its metadata guid finds nothing so my assumption is it's not actually used anywhere in the game.

But there's more! I found an actual third level within the classroom game!

There is an additional level internally called MEAT. You can access it by clicking on these four letters in the main menu (left-to-right / "reading" order):
This makes a third ENTER button appear in the middle.
The letters spell out "MEPM" btw, doesn't seem to be relevant.
Oh, the three letters that make the corrupted classroom level appear spell "LSM" but it doesn't seem to matter either.

Anyway, this is where we start.
Well holy moly.

The level is essentially one moderately large open room
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Unfortunately this is pretty much it. You can go left or right from the starting point but both lead to unfinished-looking dead ends. I also was unable to find anything interactable through the level editor (buttons, triggers, anything) - it seems it's just you the player, some weird visual effects, and static solid level.

Best I can tell you is the level was simply not finished. It's still in the game with an obscure way to access it, but there are absolutely no hints to even its existence anywhere in or outside the game. Except maybe page8 texture, which itself merely exists in the game resources and is not used on any surface in the actual game.

Regardless, here's a full video demonstration of the level.
https://youtu.be/aDK3BVzhY-s

Thank you for reading my guide.

Feel free to tell us how you interpret all the clues and lore!

Like I mentioned earlier I'm kinda better at cipher-cracking and datamining than theory-crafting so I leave it up to you folks.