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So, you want to make a GBA Pokemon romhack? There are two methods to making a romhack: binary hacking and decomp hacking. Binary hacking is the traditional kind of romhacking where you use various programs to edit a ROM file. Decomp hacking is a newer method where you make changes to the game's decompiled source code and assets, and compile them to produce modified ROMs.

Decomp hacking is generally the better method as it gives you all of the game's data and code in an easy to edit format, allowing for modifications that would be extremely difficult to implement with binary hacking. Decomp hacking also has better tools and lets you avoid many of the data corruption pitfalls of binary hacking. However due to being newer there's less tutorials for the decomps and the installation process is more complicated than with binary hacking.


====================== DECOMP HACKING ======================

First, you need to decide which ROM you want to hack. Emerald is the best choice as basically all decomp hacking resources are for Emerald and its decomp is more documented than the others.
The other decomps are also fully usable, and viable if you either want to make a really vanilla hack without custom features, or you are fine with programming/porting those features from pokeemerald by yourself.

Decomp repositories:
https://github.com/pret/pokeemerald
https://github.com/pret/pokefirered
https://github.com/pret/pokeruby

The first thing you need to do is to download a decomp and install its dependencies so that you can compile it.
Each decomp comes with installation instructions in a file called INSTALL.md.

Alternatively you can follow one of the many installation tutorials on pokecommunity:
https://www.pokecommunity.com/showthread.php?t=432351
https://www.pokecommunity.com/showthread.php?t=425246
https://www.pokecommunity.com/showthread.php?t=454082
https://www.pokecommunity.com/showthread.php?t=446273
https://www.pokecommunity.com/showthread.php?t=426921

If you want your hack to include Pokemon, items, moves, abilities or mechanics from later generations, you should install pokeemerald-expansion:
https://www.pokecommunity.com/showthread.php?t=432321
https://github.com/rh-hideout/pokeemerald-expansion

Once you've managed to compile a GBA file you can actually start making changes to the decomp.
To edit the decomp, you'll need some tools:
- Text editor: any text editor will do.
- Image editor: should support PNG format, transparency and indexed colors. (e.g. GraphicsGale, GIMP)
- Porymap: https://github.com/huderlem/porymap/releases

You can find other useful tools here:
https://github.com/pret/pokeemerald/wiki/Useful-Modding-Tools

Useful links:
Porymap manual: https://huderlem.github.io/porymap/index.html
Scripting tutorial: https://www.pokecommunity.com/showthread.php?t=416800
Pokeemerald wiki's tutorials: https://github.com/pret/pokeemerald/wiki/Tutorials
Pokecommunity tutorial section: https://www.pokecommunity.com/forumdisplay.php?fn=decomp-resources
Simple modifications: https://www.pokecommunity.com/showthread.php?t=416647 and https://www.pokecommunity.com/showpost.php?p=10354961

Team Aqua's Hideout tutorial videos: https://www.youtube.com/playlist?list=PLLNv9Lq6kDmTIYfN5NvgQRvfOHTOXl0uU
Mantager's tutorial videos: https://www.youtube.com/playlist?list=PLnf38dBXTIP2hWTp80nXY_mJM5BIOencf


====================== BINARY HACKING ======================

First, you need to decide which ROM you want to hack. FireRed is the best choice because it has the most resources and tutorials. Emerald is also viable but it's less supported than FireRed. Emerald is mostly hacked with the decomp and many of its resources are not available for binary hackers. All the other versions are shit and no one hacks them.
Once you've chosen FireRed, make sure you get the English 1.0 version of the ROM as most resources and tools expect you to use that version. 


Download the following tools:
http://getam.no-ip.info/?ver=1.92 - Advance Map
https://github.com/Gamer2020/Unofficial_XSE/releases/tag/v1.1.1 - XSE
https://www.pokecommunity.com/showthread.php?t=428388 - HexManiacAdvance (HMA)

The above three tools are basically all you need to make a hack. There are loads of other tools but their functionality is mostly replaceable with one of the previous tools (mostly HMA).

Other tools:
https://www.pokecommunity.com/showthread.php?t=320113 - Generation 3 Hacking Suite
https://www.pokecommunity.com/showthread.php?t=311461 - Generation 3 Tools
https://serenesforest.net/forums/index.php?showtopic=26913 - GBA Graphics Editor
https://www.pokecommunity.com/showthread.php?t=149454 - Nameless Tile Map Editor
https://www.pokecommunity.com/showthread.php?t=85025 - Advanced Palette Editor
https://www.pokecommunity.com/showthread.php?t=205687 - Nameless Sprite Editor Classic
https://www.irfanview.com/ - IrfanView
https://www.pokecommunity.com/forumdisplay.php?f=490&prefixid=fg_resource_tool&tag=rom-hacking - More tools
 

You might then want to check out some tutorials on getting started:
https://www.pokecommunity.com/showthread.php?t=369646
https://www.pokecommunity.com/forumdisplay.php?f=66
 
Scripting:
https://www.pokecommunity.com/showpost.php?p=9705229
https://www.pokecommunity.com/showthread.php?t=164276
FireRed flags: https://github.com/pret/pokefirered/blob/master/include/constants/flags.h
FireRed variables: https://github.com/pret/pokefirered/blob/master/include/constants/vars.h

Tile editing: https://www.pokecommunity.com/showthread.php?t=193377
Editing cries: https://www.pokecommunity.com/showthread.php?t=293830
Editing battle backgrounds: https://www.pokecommunity.com/showthread.php?t=302401
Adding new Balls: https://www.pokecommunity.com/showthread.php?t=326311
Tilesets and tilemaps: https://www.pokecommunity.com/showthread.php?t=298030
Adding the Gen 4 Physical / Special / Status split: https://www.pokecommunity.com/showthread.php?p=7465618#post7465618 and https://www.pokecommunity.com/showpost.php?p=6976957&postcount=114
 
 
FIRE RED EXCLUSIVE:
Complete FireRed Upgrade (CFRU): https://www.pokecommunity.com/showthread.php?t=425447
Title Screen Hacking: https://www.pokecommunity.com/showthread.php?t=459583 and https://www.pokecommunity.com/showthread.php?t=325944
Pokédex Expansion: https://www.pokecommunity.com/showthread.php?t=318569
Adding new types: https://www.pokecommunity.com/showthread.php?t=313872
Creating new items: https://www.pokecommunity.com/showthread.php?p=7202888
 
EMERALD EXCLUSIVE:
Title Screen Hacking: https://www.pokecommunity.com/showthread.php?t=283345
Pokédex Expansion: https://www.pokecommunity.com/showthread.php?p=9446220
Rombase: https://www.pokecommunity.com/showthread.php?t=451990
 
Other resources:
https://www.pokecommunity.com/showthread.php?t=267728 - Resized all Gen 4 and 5 sprites to 64x64, as well as Gen 4 sprites of Gen 1, 2 and 3 sprites
https://www.pokecommunity.com/forumdisplay.php?f=490&tag=binary