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I've been deep down the rabbit hole on this one for a few weeks now and finally managed to scrape the information I needed from the various places on the Internet so I could cobble together some fairly rough instructions on how to mimic what ShadyPenguinn, UnitedGamer, Patterrz, GameboyLuke, Vintendo, Original151, and ShortTempered do for their "Then We Fight" videos. They don't tell you what they use, so the below guide is a "best guess", and frankly, it looks like there's a LOT of legwork being done in the background of their videos (which tracks, because I've heard Shady mention that someone else generates the random sets and curates them for duplicates before they start filming), but I think this gets us there.

YOU WILL WANT TO HAVE MULTIPLE "PROFILES" IN YOUR EMULATOR FOR THIS. I advise a "ShinyStarters" profile and a "HackmonBattles" profile, in addition to whatever your main/normal profile is.

IN ORDER TO HACK YOUR SPECIES FILE, YOU WILL NEED TO INSTALL WARFRAME TEMPORARILY. It's like 50GB, so start now if you want to save time later. You cannot skip this step.

GET RYUJINX AND POKEMON S/V READY:
  1. Install Ryujinx and get Pokemon S/V working - I will not be explaining this step futher, there is plenty of good information on Google
  2. Create a new Profile in Ryujinx, call it "TestProfile" or something, make sure it's selected
  3. Launch S/V (should be a new game), and play until you are about to choose your starter, then save and quit
  4. In Ryujinx, right click S/V and choose "Open User Save Directory"
  5. Copy the file called "main" somewhere else - this will be your backup so you can skip the intro in the future
  6. Any time you want to reset to this point, just drag your backup into the directory
  7. Open Ryujinx, right click Pokemon S/V, and choose "Extract Data > RomFS"
  8. Put the extracted data in a folder called "romfs" somewhere you won't lose it. You'll need it later.
  9. Delete the "system" folder from the new "romfs" folder.
RANDOMIZE YOUR STARTERS:
  1. Download and unzip Gonzalooo's S/V randomizer from github "/Gonzalooo/Pokemon-Randomizer/releases"
  2. Run "PokemonRandomizer.exe"
  3. Click the picture in the middle, configure the randomizer however you want, and then click "Start Randomizing"
  4. Your randomized mods are in the "...\SVRandomizer\RandomizersAll" folder
  5. Open Ryujinx, right click Pokemon S/V, choose "Open Mods Directory"
  6. Move the newly created randomizer folder into the mods directory
  7. In Ryujinx, right click Pokemon S/V, choose "Manage Mods"
  8. Activate the randomizer folder you just added (it may be active by default)
  9. Launch S/V
PREPARE TRINITY MOD LOADER:
  1. Begin installing Warframe from Steam (mandatory step, you can get rid of it later)
  2. Download and unzip TrinityModLoader ("nightly" version) from github "/pkZukan/gftool/releases"
  3. In your Steam Library, right click Warframe and choose "Browse Local Files"
  4. Navigate from there to "..\Warframe\Tools\Oodle\x64\final"
  5. Copy the file "oo2core_9_win64.dll" into your TrinityModLoader folder
  6. Rename the new file to "oo2core_8_win64.dll"
  7. Uninstall Warframe
  8. Run "TrinityModLoader.exe" - close the various errors you may get
  9. Go to File > Open RomFS folder, and select the "romfs" folder you created via exporting from Ryujinx in the first block above
  10. Go to File > Set Output Folder, and create a folder somewhere called "TrinityOutput"
  11. TrinityModLoader is ready to use
HACK YOUR POKEMON SPECIES DATA:
  1. Download and unzip ProjectSky from github "svfeplvce/ProjectSky/releases" or gamebanana "/tools/11558"
  2. Run "ProjectSky.exe"
  3. Make any edits you want, SAVE, and click the Back button (top left)
  4. Navigate to the "out" folder in your ProjectSky folder, remember where this is
  5. Launch TrinityModLoader - it should auto-load your S/V romfs folder from last time
  6. Click "Add mod (.zip)", and select the zip folder found in the "out" folder from step 4
  7. Check the box next to the new mod that should've appeared in the left column
  8. Click "Apply Mods"
  9. Find your new mod package in the TrinityOutput folder you created earlier (or it may open automatically)
  10. Navigate to your Pokemon S/V mods folder, and create a new folder there called "ProjectSky"
  11. Drag the "romfs" folder from your TrinityOutput folder into your new "ProjectSky" folder
  12. In Ryujinx, disable any other mods, and enable your ProjectSky mod
  13. Your species overrides should now be active
HACK POKEMON INTO A DIFFERENT SAVE PROFILE
  • Acquire PKHeX and use it to hack your desired team into A COPY OF the save data from your main profile (back up your save data first so you can revert later).
  • Exact steps not included because I haven't done this part myself yet.

OTHER INFORMATION:
  • If you notice ProjectSky not saving or not exporting changes, just delete the entire folder and unzip a new one to start from scratch. The project was scrapped before completion, so it's still buggy. Hold onto the zip file as a backup just in case.
  • TrinityModLoader is needed when you plan to combine mods. Since I'm only randomizing my starters, I didn't use it for that, but that means I need to disable my randomized starters "mod" in order for other mods to work (because I didn't use Trinity to properly combine them).
  • If you wish to randomize your entire game, you will need to use TrinityModLoader to merge your randomizer's output with your ProjectSky output (so you don't need to disable the randomization when you enable the species overrides).
  • You can create a large batch of randomized starters all at once, put all those folders into the mods folder, and activate only one folder at a time (via "Manage Mods") to very quickly look at each set, and then disable the randomizer and go hack your chosen team into your main game after!
  • If you create a new profile and play the game through the intro, you can save right before starter selection and use this profile as a way to only see the randomized starters, and then switch profiles and import your selection into the battle profile.