Encryption
On the 3DS savegames are stored much like on the DS, that is on a FLASH chip in the gamecart. On the DS these savegames were stored in plaintext but on the 3DS a layer of encryption was added. This is highly likely a streamcipher, as the contents of several savegames exhibit the odd behaviour that xor-ing certain parts of the savegame together will result in the plaintext appearing.
The reason this works is because the streamcipher used has a period of 512 bytes. That is to say, it will repeat the same keystream after 512 bytes. The way you encrypt with a streamcipher is you XOR your data with the keystream as it is produced. Unfortunately, if your streamcipher repeats and you are encrypting a known plaintext (in our case, zeroes) you are basically giving away your valuable keystream.
So how do you use this to decrypt a savegame on a 3DS? First off, you chunk up the savegame into 512 byte chunks. Then, you bin these chunks by their contents, discarding any that contain only FF. Now look for the most common chunk. This is your keystream. Now XOR the keystream with your original savegame and you should have a fully decrypted savegame. XOR with the keystream again to produce an encrypted savegame.
Wearleveling
The 3DS employs a wearleveling scheme on the savegame FLASH chips. This is done trough blockmaps and a journal. The blockmap is located at offset 0 of the flash chip, and is immediately followed by the journal. The initial state is dictated by the blockmap, and the journal is then applied to that.
The blockmap structure is simple:
struct header_entry { uint8_t chksums[8]; uint8_t phys_sec; uint8_t alloc_cnt; } __attribute__((__packed__));
The journal structure is as follows:
struct sector_entry { uint8_t virt_sec; // Mapped to sector uint8_t prev_virt_sec; // Physical sector previously mapped to uint8_t phys_sec; // Mapped from sector uint8_t prev_phys_sec; // Virtual sector previously mapped to uint8_t phys_realloc_cnt; // Amount of times physical sector has been remapped uint8_t virt_realloc_cnt; // Amount of times virtual sector has been remapped uint8_t chksums[8]; } __attribute__((__packed__)); struct long_sector_entry{ struct sector_entry sector; struct sector_entry dupe; uint32_t magic; }__attribute__((__packed__));
With magic being a constant 0x080d6ce0.
Partitions
There can be multiple partitions on the chip. For some games one is a backup partition, some other games seem to use only one partition, yet other games actually use multiple partitions.
Filesystem
Savefiles are stored on the FLASH in a custom filesystem called SAVE. SAVE has a header which describes where the various bits of the filesystem live. The most important is the FST or filesystem table. You can find the FST by first finding the file base offset which is the offset to which all the entries in the FST are relative. The file base offset is a uint16_t at 0x58 from the filesystem start. The FST offset is a uint32_t at 0x6C and is in blocks (which are 0x200 bytes large).
Once you've found the FST, parsing it is fairly straightforward.
struct fs_entry { u32 node_cnt; u8 filename[0x10]; u32 index; u32 unk1; // magic? u32 block_offset; u32 file_size; u32 unk2; u32 unk3; // flags and/or date? u32 unk4; }
The first entry is the root directory, easily identifiable by the node_cnt being larger than 1. The node_cnt includes the root directory itself, so there are node_cnt - 1 files in the root directory. The entries that follow after the root directory are the actual files. Reading them out is as simple as taking the file base offset and adding (block_offset * 0x200) to it.
Example from Super MonkeyBall 3D:
0003800: 04000000 21000000 00000000 00000000 ....!........... 0003810: 00000000 00000000 00000000 00000000 ................ 0003820: 00000000 00000000 00000000 00000000 ................ 0003830: 01000000 736d6233 64732e64 61740000 ....smb3ds.dat.. 0003840: 00000000 00000000 d57b1100 05000000 .........{...... 0003850: e4060000 00000000 c8cf0008 00000000 ................ 0003860: 01000000 6d677265 706c6179 30302e64 ....mgreplay00.d 0003870: 61740000 01000000 d57b1100 09000000 at.......{...... 0003880: 1c210000 00000000 cd331000 00000000 .!.......3...... 0003890: 01000000 6d677265 706c6179 30312e64 ....mgreplay01.d 00038a0: 61740000 02000000 d57b1100 1a000000 at.......{...... 00038b0: 1c210000 00000000 00000000 00000000 .!..............