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Works flawlessly out of the box.
Played in on-line multiplayer on Steam Controller, no issues.
Megaton Edition has serious issues detecting the Steam Deck's controls in both gamepad and KB+M mode; in gamepad mode, right trigger doesn't fire your weapon. In KB+M mode, mouse aiming is unresponsive. There is no support for mixed input.
By default, Megaton Edition has major issues properly detecting the Steam Deck's controls. By installing eduke32 via Luxtorpeda, you can avoid these issues and enjoy a seamless experience.
Go into desktop mode, open the "Discover" application, download ProtonUp-Qt, and add it as a non-Steam game. Once you've done this, you can activate it in gaming mode to install Luxtorpeda. Select Luxtorpeda as your preferred compatibility layer for Megaton Edition, and you'll be prompted to use eduke32 to play when booting the game. Once you've done this, you're good to go!
Clicked install, then play and it all worked sweet! just like actually playing on DOS
Game runs just as good as it did on windows.
Not frequent and very mild crackling sound. Didn't notice if it went away or I got used to it considering it was barely noticeable.