1. Be in Desktop mode download innoextract linux binaries and right click innoextract-1.9-linux.tar.xz and go to Extract->Extract archive here, autodetect subfolder.
   
2. Download the patch can't link but use google and it must be called (MuvLuvAlternative_DirectorsCut.exe).
   
3. Right click in download folder and click "Open terminal here" and copy without the parentheses (cd ~/Downloads) into it and press enter.
   
4. Copy (/home/deck/Downloads/innoextract-1.9-linux/innoextract /home/deck/Downloads/MuvLuvAlternative_DirectorsCut.exe) again without the parentheses into the terminal and press enter and wait for that to complete.
   
5. Go to (/home/deck/Downloads/app) and get the alternative16.rio.ruo1 file and move it to (/home/deck/.local/share/Steam/steamapps/common/Muv-Luv Alternative) or you can right click the game then go to Manage->Browse Local Files.

If you can't find .local folder is because it is hidden by default so you have to go to the 3 lines then click "Show Hidden files."
Hope this helped. This is my first guide so sorry if it is sloppy.