If you attempt to copy a 4+ gigabyte file to your jailbroken 3DS's SD card, you will have gotten a perplexing message about the file being too large for the filesystem. This does not refer to the capacity of the SD card (which can be anywhere from 16 to 128 GB), but the filesize limit that is baked into the FAT32 standard. Games such as Pokémon Ultra Sun / Ultra Moon can trigger this error, and it can be quite demoralising. However, as with all things FOSS, there are always ways around problems like this.
Most people's first impressions would be to reformat the SD card to something with greater file allocation, but this is not supported here. All systems in the Nintendo 3DS line are compatible with FAT32-formatted SD cards only, so don't waste your time formatting to NTFS or exFAT. This won't work here.
Instead, we need to involve a program called hShop— the replacement for the Nintendo eShop. The hShop has all the same content that the eShop did, in a text-only environment so it doesn't waste a lot of time loading irrelevant eye-candy. Likely due to some reason related to piracy, hShop can't be downloaded from the UniStore, so we'll need to use FBI in a rather unconventional way.
Open the hShop website* and scroll down until the QR code is fully displayed on your screen. You can use any web-capable device for this, including smartphones, since the only thing we need from here is the QR code. FBI on the 3DS does the rest.
Open FBI, then scroll down to "Remote Install". Select this, then select "Install from QR Code". Point your exterior cameras at the QR code from the hShop website. The program should immediately recognise and decrypt the code. If it doesn't, use a cloth to wipe any dirt away from the camera lenses. Press "A" when prompted to install it. When finished, return to the homescreen and open the present with the hShop Client in it.
* - Why is there no link here?
Because, technically, this is a pirate site. Even though the 3DS games and DSiWare available there are abandonware, the Virtual Console games are not, with most of them being currently available on Nintendo Classics. I would rather not link to pirate sites directly because of the nature of AI-based web crawlers. The analytical kind are able to make inferences based on a site's content and, well, I talk a good deal about datahoarding and copyright liberation on this site, so... yeah. We'll have to make do with searching it out on searXNG. Loose lips sink ships.
On the hShop screen, you will see a number of options.
• Games: 3DS titles released on the eShop.
• Updates: Program revisions for installed titles. You need to install the game before you can update it.
• DLC: DLCs for installed titles, such as Lucas and Ryu for Super Smash Bros.
• Virtual Console: Retro games released through Virtual Console. To install games on your system not released on VC, you will need to run either a console emulator or, in the case of Game Boy Advance games, a Win32 program called New Super Ultimate Injector. Details on this procedure can be found at the Hacks Wiki
• DSiWare: Small games and programs released for Nintendo DSi.
• Videos
• Extras: Developer tools, game hacks, and other uncategorised content.
• Themes: Cosmetic modification for the 3DS homescreen and menus.
At the moment, we want Games, so select that, then choose the region the game you want was released in (if released in multiple regions, select yours). If you know the title, search for it. Otherwise, scroll through the available titles until you find it, then press A to select it, and A to install it.
The install procedure only pulls in data at a rate of hundreds of kilobytes per second, so this will take a long time. Potentially several hours depending on your internet connection. Fortunately, the newest version of the hShop Client software can continue downloading and installing while the screen is off, or you can connect the 3DS up to power; also, the software is smart enough to remember where it left off if your connection should be interrupted.