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This may sound rather weird but I promise it worked when everything else didn't.
To start off, I have been fighting for days trying to get System Shock 2 running with the tool and mods; and it has been a nightmare. Every time I ran SS2Tool it would just wipe a bunch of files including the EXE for the game.

My OS is Garuda Linux (based on Arch BTW lol) main thing that matters though is having Heroic Game Launcher and of course Rsync.

Step 0: download all the stuff you need, including the game installer since if you mess up you may have to try again.
In Heroic, I just used the standard Wine Default (9.12 Staging) Install the game (obvi) then launch it once just to make sure everything is working.

Step 1: allow Rsync through your firewall.

Step 2: drop the SS2Tool into the game folder in the Heroic Prefix.

Step 3: in the Heroic settings menu for the game hit Run EXE On Prefix, find the tool and run it. Yes it will probably "delete" a bunch of stuff including the game exe but that's OK, that is what this guide is working around. My suspicion is because the GOG version includes "fixes" that the tool can't properly read everything since we are also on Linux; don't know why, i'm not a SWE or L337 H@xx0r just a nerd who plays games.

Step 4: go into the SS2ToolSyncBackup folder, copy everything in there and paste it all back into the main folder, you should notice an overall lack of overwrites.

Step 5: run the SS2BMM mod manager, it should detect the game's executable which means you're good.

Step 6: use SS2BMM to mod the game and enjoy. Whenever you want to change your mods, just use Run EXE on Prefix to launch SS2BMM.

So far I haven't run into any issues or crashes and have played several hours now and gotten to Hydroponics already.
Attached is a picture for proof, yes it is back at start because I was doubling back for something lol.
Post edited October 05, 2024 by IgnisEtAequitas
we are aware some people won't be able to use the tool, so if you have the current GOG/steam build, you just need to get the mod manager exe, run that, load SCP (the Community Patch), and as long as you keep that active, 99% of mods will work ok.