download the latest release here
http://www.gateway-3ds.com/downloads/
copy the launcher.dat onto your sd root.
hold the button you set as the gw boot and once you see a dragon on the top screen hold select and L
over over to the option that says format emunand and press A. press A again if prompted
insert your gateway cartridge into your 3ds and press a on the farthest option to the left.
if you already have tha cart in when you boot into gateway later it will completely skip the menu and boot up your emunand
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3ds root. the msd in the gateway cart it for roms cheats and the sort