Final Fantasy IX is Unsupported on the Steam Deck
FFIX is unsupported on the Steam Deck, but has a Gold rating on protondb. Honestly, it runs perfectly out of the box. There is no tinkering needed.
Moguri Mod for Final Fantasy IX on the Steam Deck
Moguri Mod is a massive 11gb upgrade to FFIX. It includes all new HD backgrounds, HD textures, and a beautiful soundtrack.
I followed a writeup by Inkerlink on Reddit.
In summary, once you download the mod, you just need to add the .exe file as a Non-Steam Game in the Steam Client in desktop mode. From there, you can run the installer and it will unpack all of the Moguri Mod files.
The key thing for me was, since I have a 64gb Steam Deck there wasn’t enough space to install FFIX and the Moguri Mod without an SD Card. Thankfully, Inkerlink included directions on how to install if FFIX is installed somewhere other than the default location.
From here, I relaunched in handheld mode and just launched FFIX. The Moguri Mod config came up and you can play with the options there.
Moguri Mod also allows for widescreen gameplay!
