You'll be able to use any mod you want, even those that say they're not Ironman compatible.
This way you can still earn achievements while playing the way you want.

I personally only use purely visual and UI mods, but some of them change the checksum...which is a bit annoying.

First, go to your Stellaris directory and make a backup of the stellaris executable
I recomend saving it to another folder or just rename the extension to .old (make sure extensions filetypes are visible/enabled in Windows)

Windows:

• Microsoft Word
  
• Notepad++ [notepad-plus-plus.org]
  
• HxD[mh-nexus.de]

Linux:

• Nano (It just works. Gedit and Notepadqq would crash/get unresponsive)
  
• Okteta[apps.kde.org]

A friend of mine @r0fld4nc3 is working on improving a project that automates the process.
The patcher does the same, finds the hex values and replaces the bytes it in order to enable Achievements with mods.

You can find the Patcher project on the Stellaris Checksum Patcher GitHub[github.com].

It is important to use the Pre-Release 2.0.0 or higher[github.com] for the most recent versions of the game, as this version is capable of providing and fetching the most recent patches as the game is updated and the patching process eventually breaks.
It now (as of Pre-Release 2.0.0) supports Windows, Linux and MacOS versions of Stellaris.

If you find that the Patches are failing to apply on a new game version release, please be patient and wait a bit until the updated patterns become available, as that is a manual process that must be updated by the developer or community.

In case that you are able to find the byte pattern to patch, feel free to open an Issue and it will get tested and implemented as soon as possible.

Otherwise, check back at a later date if that's the case :)

Any feedback and/or issues are best addressed in the GitHub Issues page.

Note: Values possibly deprecated. Check Automated Patcher[github.com] or manual decompilation guide by class101

First make sure Stellaris isn't running

Open HxD then go to File -> Open and choose the Stellaris.exe

CTRL+A (to select everything) and copy everything to a blank Word file.

Make sure you have the text cursor in the beginning of the document.
Then just do CTRL+F (find/search) and go to advanced find



Enable "Use wildcards"



In the search you can use this:
48 8B 12 ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? 85 C0

When you find it on word, copy that value



Go back to HxD (with the opened Stellaris.exe)

Search->Find->Hex-values-> Paste the value you just copied from Word and then click "Search All"

After you find the value, change the 85 C0 to 33 C0. Save it and replace the original executable.

Note: Values possibly deprecated. Check Automated Patcher[github.com] or manual decompilation guide by class101

Make sure Stellaris isn't running

Open HxD then go to File -> Open and choose the Stellaris.exe

CTRL+A (to select everything) and copy everything to a blank Notepad++ file.

Make sure you have the text cursor in the beginning of the document.
Then just do CTRL+F (search->find) and tick at the bottom "Regular Expression"

In the search you can use this and then "Find Next":
48 8B 12 .. .. .. .. .. .. .. .. .. .. .. .. .. .. 85 C0



When you find the value, copy it

Go back to HxD (with the opened Stellaris.exe)

Search->Find->Hex-values-> Paste the value you just copied from Word and then click "Search All"

After you find the value, change the 85 C0 to 33 C0. Save it and replace the original executable.

Note: Values possibly deprecated. Check Automated Patcher[github.com] or manual decompilation guide by class101

First make sure Stellaris isn't running

Open Okteta, click "Open" and choose the stellaris executable.
CTRL+A (to select everything), RIGHT-CLICK and select "Copy As"->"Values". In the "Separation" box, remove any space there and then "Copy to Clipboard"



Open your Terminal and enter:
nano hex.txt

Paste your previously copied values to it (CTRL+SHIFT+V)
It will take some time, just wait around 30 secs max

After the values show up, do CTRL+W (Where Is) and ALT+R (Reg.exp.)
Paste the following and enter:
488B30......................................85DB



The value will be highlighted for a few seconds. Copy it.



Go back to Okteta with the stellaris executable opened, CTRL+F and paste the hex value



After you find the value, change the 85 DB to 31 DB. Save it and replace the original executable.

Note: Values possibly deprecated. Check Automated Patcher[github.com] or manual decompilation guide by class101

Since the Proton version is basically the Windows version with a compatibility layer, you can follow the Linux (Native version) steps but use this value instead:
488B12............................85C0

And change the 85 C0 to 33 C0

If you can't find the value above, you can shorten the amount of ?? or .. you use on your expression
? or . represents one character, any character. So ?? or .. is two characters.

This value can vary depending on your memory allocation, so you can shorten or lengthen the amount of "??" or ".." depending on the program you use

Examples to try (Windows):
48 8B 12 ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? 85 C0
48 8B 12 ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? 85 C0
48 8B 12 ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? ?? 85 C0

Examples to try (Linux):
488B30....................................85DB
488B30..................................85DB
488B30................................85DB

And so on, you get the gist

The Hex value you want to search for always begins with
48 8B 12 and always ends with 85 C0 Windows
48 8B 30 and always ends with 85 DB Linux

If this method ever gets outdated (it can happen due to the way it works) or somehow it just doesn't work for you, you can try and use this guide from class101

It's more time consuming imo and "complicated", especially if you aren't very tech-savvy.
But it's an excelent guide regardless and should be more future proof than what I posted here. (Unless Paradox manages to get some way around it, which I doubt).

The original game executable is probably signed with a Digital Signature. This means that your AntiVirus will try and check this Digital Signature on its database to validate its checksum.
Basically, a checksum is a sequence of numbers and letters used to check data for errors and is calculated by the hex values/bytes. It gives a unique identifier ID to your program let's say.
But since you're altering the executable itself with hex editing, the checksum it'll produce will be different from the original exe, thus creating a false positive for antiviruses when they try to validate it.