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This tutorial will try to help you extract a 3DS|CIA|CXI file to change its content, and will also explain how to rebuild your game once edited.

Thanks a lot to Ericzander & BullyWiiPlaza for their help to translate this tutorial in english
(Because I'm French, it’s difficult to make a full tutorial in a good english...).
If anyone see any typo or something wrong with my english (in the setup, the script, the tutorial...) let me know!

Ce tutoriel est également disponible ici pour les français (Pas à Jours) :
This tutorial is also available here for french users (Outdated):
http://www.pokemontrash.com/jeux-pokemon/decrypter-compiler-rom-3ds.php

SUMMARY

- What you need
- Prerequisites
- Decrypting
- Extracting
- Editing
- Rebuilding​

What you Need

• A 3DS|CIA|CXI File (It can either be a game, game's update, system application, but anyways not a DLC file nor a DSi Ware!)
• WinRAR, or another archive extractor
• HackingToolkit9DS -> Click Here

Prerequisites

Install the new SetupUS|FR.exe of HackingToolkit9DS as a common tool:

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Extracting

Open HackingToolkit9DS:


Don't forget, your file(s) should not have any spaces in its(their) name(s), nor special characters, like é or à.
You want extract PokemonMoon.3ds ? Just write PokemonMoon.

If you plan to extract a 3DS file:
Write the "D" command, and enter the name of your .3DS file WITHOUT its extension.

If you plan to extract a CIA file:
Write the "CE" command, and enter the name of your .CIA file WITHOUT its extension.

If you plan to extract a CXI file:
Write the "CXI" command, and enter the name of your .CXI file WITHOUT its extension.

You are asked if you want decompress your code.bin file, choose (n/y).
Wait while it's extracting.

The ExeFS content will be extracted in an ExtractedExeFS folder.
The RomFS content will be extracted in an ExtractedRomFS folder.
The DownloadPlay content will be extracted in an ExtractedDownloadPlay folder.
The Old3DS update will be extracted in an ExtractedO3DSUpdate folder.
The New3DS update will be extracted in an ExtractedN3DSUpdate folder.
The Manual will be extracted in an ExtractedManual folder.
The 3D Banner will be extracted in an ExtractedBanner folder.

The work here should be ok.
Now you’re able to edit the game, go to Editing.

Editing

Do what you want.
Edit music, textures, banner, icon..
If you follow this tutorial, you know what you want to do.
Once it's finished, rebuild your game.

Rebuilding

If you extracted and plan to rebuild a 3DS file:
Open HackingToolkit9DS, write the "R" command, then enter the name you want for the output file.


Once done, don't forget to encrypt it using Decrypt9.
Open Decrypt9 using the method of your choice, choose Content Decryptor Options, then NCCH/NCSD File Options and finally NCCH/NCSD Encryptor.

Enjoy!

If you extracted and plan to rebuild a CIA file:
Open HackingToolkit9DS, write the "CR" command, then enter the name you want for the output file.

Once done, and only if you have dealed with a system application (HomeMenu, SystemSettings, etc...) you need to encrypt the CIA back before install it.
Start Decrypt9, choose Content Decryptor Options, then CIA File Options and finally CIA Encryptor (NCCH).

Enjoy!

Troubleshooting

Before report an issue, be sure:
- Your 3DS/CIA/CXI file doesn't have any space or special caracter in its name (such as é or à).
- Your 3DS/CIA/CXI file is in the same folder as HackingToolkit9DS.
- You're not trying to extract the file in the ProgramFiles folder (where installed core files are).
- To write or don't write the extension of your file when specified.
- To have installed the setup package for your langage (SetupXX.exe file).

Changelogs

Version 10
- Added: Support for Boot9 extraction on PC. Absolutely no more decryption is required on 3DS.
- Renamed: Project is renamed HackingToolkit9DS for the occasion.
- Edited: Some strings, words and sentences has been changed.
- Removed: Temporarily removed the 32 bits support.
- Removed: Integrated 3DS Builder.
- Removed: Integrated Pokemon Patch Pointer Tool.
- Removed: Integrated RomFS Extractor.
- Removed: Integrated RomFS Builder.

Version 9
- Fixed CIA rebuild script.

Version 8
- Fixed MassExtraction and MassRebuild scripts.

Version 7
- 32bits support should be fixed (I forgot to include a 32bits build of MakeRom).

Credits and Thanks

Credits:
CtrTool : profi200 | 3DSGuy| Neimod
Makerom : profi200 | 3DSGuy
Decrypt9 : d0k3, Shadowtrance & Archshift
HackingToolkit9DS : Asia81
CleanTool9 : Asia81

Thanks to:
Megadrifter
Stratovarius
Reisyukaku
Guitoh
Weby
Apache Thunder
Ericzander
BullyWiiPlaza
Cellenseres​

THE LAST WORD

AS ALWAYS #TEAMONODERA AND #TEAMREM UNTIL THE DEATH

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--sorry for my bad english--
i did all of these step ,when i rebuild Kingdom hearts 3d (with rsf editted) ,it created a 3ds rom has smaller size than it was (2,1gb -> 1.8gb)
Load the rom on 3ds and nothing happen (the icon is blank)
Tried to use this tool
https://gbatemp.net/threads/tool-makerom-gui.376540/
and this is error it give me

 

Proof it's working :

Just read the tutorial.

I'm sorry, but i don't really know how to do this with other game such as Pokemon.
Give me your RSF, i will try it.
It's Kingdom Hearts 3D EUR ?

 

I haven't US version, i will download it later

 

What's your game ?

I will try to make a video tutorial if he can help someone

 

Just read the tutorial?

Here a video to show you it don't work for me and i don't know for other (Video edited because I forget to not show the 3ds key):


What is wrong? I don't understand!

 

WtF ?

 

I know, but where i give a 3DS key oO ?
My slot0x25KeyX.bin in the pack is not blank ?

 

fail, removed.

 

and now ?