Make sure you have emuNAND set up - Can be created from the GW menu when you launch it.
1. Download BigBlueMenu.3ds or DevMenu.3ds - Place on SD card for GW
2. Download BigBlueMenu.cia or DevMenu.cia - Place on internal SD card for 3DS
3. Download MultiPatcher.cia from the forums here -
https://gbatemp.net/threads/release-free-multi-patcher.391945/
4. Launch GW Mode in emuNAND and run BigBlueMenu or DevMenu ROM
5. Press right on the DPad until you see your internal SD card folder structure
6. Install the FreeMultiPatcher and BBM or DevMenu CIA files
7. Run FreeMultiPatcher from your home menu - Press Start after it launches
8. Launch eShop, make sure you can get to it, you should be able to. If not check step 7 again.
9. Go to this page on your computer, scroll to the bottom and scan the QR code in eShop -
http://en-americas-support.nintendo...-to-update-super-smash-bros.-for-nintendo-3ds
10. Install the update
11. Run GW classic mode and your cart should now be running on the latest version
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This cart is a different story. The updates aren't openly available on eShop anymore and have to be accessed while in game or right before launching the game. MultiPatcher doesn't work in classic mode unless its installed to sysNAND.