I probably should have posted this earlier back when Lethal Company was more popular, but better late than never.
For installing mods, you first need to go to desktop mode and download r2modmanPlus. You specifically want the r2modman-x.x.xx.AppImage file from the release page. You can run this app image in desktop mode to access the mod loader, and install mods for the different supported unity games. After downloading the mods you want through the built in downloader, you can click "Start Modded" in the upper left corner to start the game. It will open steam and run the game with the mods. You will usually see a command prompt window open before the game does, this both lets you know the mods are enabled and will let you see if there are any errors with the mods running.
After you've confirmed the game will run with mods in desktop mode, the next step is to get mods working in game mode. In R2modman, open the settings menu at the bottom, and look for an option that says "launch options". This will say something like --doorstop-enable true --doorstop-target "Z:/home/deck/.config/r2modmanPlus-local/LethalCompany/profiles/Default/BepInEx/core/BepInEx.Preloader.dll" -r2profile "Default". You want to copy this command, and then go to steam game properties for the game you're running and paste these launch options into the launch arguments box. If you have trouble copying the command, you may need to connect a keyboard or bind "ctrl + sub command c" to one of the deck's back buttons. Now the game should run with mods in game mode.
Troubleshooting:
If you have any trouble and the game is installed to a microsd card, you may need to move it to your internal SSD.
Sometimes the resolution of games will get messed up being launched with mods this way. Here are some suggestions if you get weird resolution scaling:
- In steam game properties, set the resolution from automatic to 1280x800.
Alternative resolution fix:
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Launch game in desktop from mod manager
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Open settings
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set display mode to "Window"
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From desktop, click top bar of window Lethal Company is running in, then right-click
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From drop down select "Maximize". Resolution should now be scaled to native.
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In game settings, select "Windowed Fullscreen", everything should work now without window borders.
This guide was largely written from memory, so I may have left out some helpful details. If you notice anything missing or have any issues let me know and I'll try to update it.