The patch is applied via or PPF patching tools. You start with a clean, unmodified God Eater 2 V1.40 Japanese ISO and apply the patch file to generate a new, playable ISO.
Search for: "God Eater 2 v1.40 English Patched ISO" or "God Eater 2 (J) [v1.40] [ENG] [PPSSPP] .iso" God Eater 2 PSP V1.40 -JPN- -English Patch- ISO
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