I have tested emulators released for Stargate 3ds for GBA, SNES, NES and GB/GBC emulation via this link, but unluckily, all the emulator icons are visible on Stargate DS mode, but none of them can really be use. Plus, the Stargate-3ds team doesn't release any exclusive emulators for GBA&SNES as they promised, so until in 2019, we have no method to use Stargate 3ds emulators to play any retro games.
But don't worry, I still find other methods to play GBA&SNES games with the help of Stargate 3ds flashcard.
There are two ways to play GBA games on 3DS via Stargate. The first one is to play the games directly using mGBA emulator. This can be done if you use Stargate 3ds card to homebrew the 3DS via any homebrew exploit, like the Ninjhax 2.9.
Guide: Homebrew any 3DS with Stargate 3ds to play GBA games
1. Go to the get ninjhax section of this page and enter your console's firmware version.
2. Submit the form; you should get your very own ninjhax QR code.
3. Download the homebrew starter kit and extract it at the root of your SD card. After this step, you should have a file named boot.3dsx placed at the root of your SD card.
4. Make sure your 3DS's wifi connection is enabled and connected to the internet (this is important!).
5. Insert Stargate 3ds card to your console. Start CUBIC NINJA on your console, choose "Create", then "QR code", and finally "Scan QR code".
6. Scan the QR Code. This step might take a couple tries; make sure you fill up as much of your 3DS's screen with the QR code. If scanning the QR code returns to menu with an error, try a few more times.
7. Follow the on screen instructions.
8. Once the ninjhax is installed to your gamecard, just go back to the "QR code" menu and it'll run automatically! you can now run homebrew apps on your 3DS! You can now use mGBA emulator to play GBA games.
The second one is to inject the games to the console using GBA VC Injector. This can be done if you use Stargate 3ds card to install a CFW to your console, such as the Luma3ds custom firmware.
Guide: Play GBA games via GBA VC Injector on 3DS CFW
Steps are showed in details from this link https://gbatemp.net/threads/release-ultimate-gba-vc-injector-for-3ds.438057/, click it, you won't miss every important step to convert the .GBA to .CIA games on play on your 3DS CFW. But don't forget, you need to install 3DS CFW via the Stargate 3ds card firstly.
Step 1 - Remove the MicroSD card from your StarGate and insert the cart into your system (You will not need it during this process).
Step 2 - Download the Easy Mode CFW .zip file from HERE and copy the contents of the “\Install CFW\Copy to 3DS SD card\” folder to your 3DS MicroSD card.

Step 3 – Place a low powered magnet on the Sleep Activation Spot for your model.
For 3DS – Place the magnet just below the B button.
For 2DS – Slide the Sleep Switch to the ON position.
For N3DS – Place the magnet to the right of the Start/Select buttons.
For N2DS – Place the magnet in the center of the A/B/X/Y buttons.
You can test the correct location by first powering on your unit and placing the magnet to see if the system goes into Sleep Mode.
Make sure to power the unit off before continuing to the next steps.
Step 4 – While holding the Start, Select, and X buttons all at the same time, press the Power button briefly and continue to hold the other 3 buttons for a short pause before releasing them. If done correctly, an Install Menu should appear. If not, remove the magnet to take the unit out of Sleep Mode and power it off before trying Step 4 again.
Step 5 – From the menu, select “Install CFW” and you will be presented with a warning about your SysNAND being locked. This is normal and you should press “Yes” to unlock it for writing.
You will receive one Final Warning before the modification takes place. It is still safe until this point to power off your console and stop the procedure. When ready, hold the X button to finalize the install.

Step 6 – Your console is now running Luma Custom Firmware! You can select the Nintendo Sound Player and it will open the Homebrew Launcher for useful tools and emulators. For Recovery Options, hold Down while powering on the system. For Cheats and more, hold L+Down and press Select from the main 3DS Menu.
Where to download GBA ROMS for your 3DS?
- https://www.emuparadise.me
- https://www.loveroms.com
- http://www.freeroms.com