Copy the Decrypt9.3dsx / Decrypt9.smdh from the output folder after building to your 3ds sd card ( /3ds/Decrypt9 ). The .3dsx and .smdh are a modified version of https://github.com/patois/Brahma with the Decrypt9 bin built in.

Then use ncchinfo_gen.py on your encrypted game (dump the game with the Gateway launcher). Or if using on cia content extracted with ctrtool use ncchinfo_tgen.py, for example extracted theme pack cia's.

Then, if you're on firmware that is less than 7.x, create/edit slot0x25KeyX.bin in a hex editor and put in the 7.x KeyX (no, I won't give it to you).

Place ncchinfo.bin (and slot0x25KeyX.bin, if on less then 7.x) on your SD card, and run the decryptor. It should take a while, especially if you're decrypting a larger game.

Run from the homebrew menu with ninjhax.

Credits

Roxas75 for the method of ARM9 code injection

Cha(N), Kane49, and all other FatFS contributors for FatFS

Normmatt for sdmc.s as well as project infrastructure (Makefile, linker setup, etc)

Relys, sbJFn5r for the decryptor