If you only have access to a 3DS, it is important that you update your DSTWO's firmware
before you update the firmware on your 3DS. If you have access to a DS phat/lite/i/XL then you can update on any of those devices without worry as long as you have the latest EOS on the DSTWO.
Firmware 1.09 - works on 3DS's on v1.1.0-1 and prior
Firmware 1.12 - works on 3DS's on v2.2.0-4 and prior
Firmware 1.13 - works on 3DS's on v3.0.0-6 and prior
Firmware 1.15 - works on 3DS's on v4.1.0-8 and prior
Firmware 1.16 - works on 3DS's on v4.2.0-9 and prior
Firmware 1.17 - works on 3DS's on v4.3.0-10 and prior
Firmware 1.18 - works on 3DS's on v4.4.0-10 and prior
Firmware 1.19 - works on 3DS's on v5.1.0-11 and prior
Firmware 1.20 - works on 3DS's on v6.1.0-12 and prior
Firmware 1.23 - works on 3DS's on v6.3.0-12 and prior
Firmware 1.25 - works on 3DS's on v9.4.0-21 and prior
1. Download the latest firmware from the top of this post.
2. Extract "dstwoupdate.dat" to the root of your microsd card.
3. Put your microsd card into your DSTwo and insert it into a DS phat/lite/i/XL or your 3DS.
4. Turn on the DS and start the DSTwo, once you get to the plugin menu it should show a popup saying "Update system *your current firmware here* - 1.25", press A here to start updating.
Make sure that you do NOT turn off or close the DS until it is finished upgrading.
5. If you did not see the popup, trying renaming "dstwoupdate.dat" to "ds2update.dat", then try it again.
You should now be on the latest Firmware, and dstwoupdate.dat (or ds2update.dat) should no longer be on your MicroSD card if it updated correctly.
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If you started the update but it didn't finish, and now the DSTwo isn't recognized, you just get "Update error, enter than wait 3 minutes"
still in the process of trying to figure out a fix, read
this thread for more info
possible fix is to download
this and extract system1.dat into your _dstwo folder, then try the firmware update again.