The 3DS core in BizHawk uses Encore, a fork of Citra. This core was added with the release of BizHawk 2.10.

3DS games come in multiple extensions that the core can run. However, there are some games that are encrypted, typically with the file extensions .3ds or .cia. While it's possible to use tools to decrypt them to make them directly playable, there are certain files that can run them without decryption.

To run encrypted 3DS games, you need the following files:

As these are not detected automatically in BizHawk, these files must be manually set. While BizHawk is open, go to Config -> Firmware... and scroll down to the Nintendo 3DS section. Right click each section and select Set Customization to have your files set. If you can't get encrypted games to run after setting those files, then it means that one or both of the files lack the correct information needed to run encrypted games correctly.

TODO: Fill out this section with information about 3DS save state sizes, save data potentially causing desyncs with save states made before a point the game saves, and other potentially important information. Also maybe rename this section's title to something cleaner