ROM Hack Pokemon Shuffle Preservation Mod v1.1

[Sirence]

I found a way to do it only using FBI, GM9, flips, Luma, and JKSM. This guide is only for those who don't have any save data or want to start over. Don't worry you don't have to change numbers with HxD like other poor souls did.

First get a cia copy of Pokémon Shuffle from the Hshop to install into your 3ds using FBI. (make sure you don't have any extra data in Data Management)

Then power off your 3ds and go into GM9 to dump it by pressing (Home), select "Title Manager", select "[A:] SD CARD", select Pokémon Shuffle, select "Manage Title..", and select "Build CIA (standard)". (should save in /gm9/out folder)

Next put the SD card into your computer use flips to patch it with the bps file and save it into the cias folder. (delete the previous dump cia from /gm9/out since its not needed anymore)
For those confused where the cias folder is, you create it yourself right next to the other files, it should not be inside another folder.

Back on the 3ds delete the first Pokémon Shuffle with Data Management and then install the new one with FBI.

Then open Pokémon Shuffle and it should be version 1.5.0 (you can check on the top right corner of the top screen when you play the game) and press Home to exit the game. (don't delete the extra data it creates as its need for the next step)

Then on JKSM go to Titles, and select Pokémon Shuffle, select New, and name it whatever you want and exit JKSM.

Then put the SD back into your computer (again) and put the savedata.bin into the /JKSM/Saves/Pokémon Shuffle/"file you named". (the bin file might already be in there but check to make sure. I didn't wanna take any chance and replaced it with the one that came with the zip file)

Then on your 3ds go to the Rosaline menu by pressing left shoulder, down d-pad, and select at the same time. Then go to "Miscellaneous options" and select "Nullify user time offset". Then go back to Rosalina Menu and select "Power off/reboot" and press Y to reboot.

Then go into JKSM, select Titles, select Pokémon Shuffle, select Save Data, select your save file by pressing Y to restore it, and finally select yes.

And you should be good to go, just complete the first 11 stages to unlock the Expert stages, before trying the Special stages. Since the creator of the mod said they can be buggy.

If it helps I tested the method multiple times and the game launches with the special stages and they work fine after completing the tutorial stages.

The cia I got from hshop and gm9 does not work with the patch. Do you have any idea what could be the issue?

 

[Kwyjor]

Do you have any idea what could be the issue?

Perhaps you should elaborate on what "does not work" is supposed to mean? Do you get an error message, or what?

 

[Sirence]

Perhaps you should elaborate on what "does not work" is supposed to mean? Do you get an error message, or what?

Oh sorry of course. The issue is that flips says that the Patch is not intended for the cia I got from hshop / gm9. The hashes also don't match. In hshop they say the Version for the game is 5.6.0 which doesn't seem right.

Post automatically merged: Apr 11, 2025

Here are my steps:
Installed the game from hshop
Boot into gm9
Navigate to the title and build cia (standard)
Go to the out folder and check the cia, it says version 5.6.0 and contents 2/2
Try to decrypt the cia, says already decrypted
Copy the cia to my pc and apply either patch 1 or patch 2
Both patches say the ROM is not the right version

Post automatically merged: Apr 11, 2025

I managed to locate the issue. I was using an older version of gm9. Updating and dumping the cia again created one usable with patch 1.

 

[locosnoob]

Hi, same happens to me, is there any known solution?

 

[Kwyjor]

Hi, same happens to me, is there any known solution?

Perhaps you should elaborate on what "does not work" is supposed to mean? Do you get an error message, or what?

 

[locosnoob]

Yes. He did that and still no special stages. I have never ever seen this issue like this happen. When I patched my game up this didn't happen to me so i'm very confused as to why this only happens to his 3DS. I even went to his house and did the installation myself and still the special stages won't appear

this is the message i tried to quote, sorry im new in this page

 

[RainingChain]

Hello,

Thanks a lot SaltedNeos for the mod. It works very well and greatly improved my Pokémon Shuffle gaming experience.

I created a webtool and a guide to ease the process of patching the game file .cia and the save data file. It is aimed towards players playing on emulator.

I can't post links yet, but you can find the webtool on my GitHub (RainingChain) in the repo PokemonShuffleSpecialStagesDLC.

Thanks,
RainingChain

 

[SaltedNeos]

Hello,

Thanks a lot SaltedNeos for the mod. It works very well and greatly improved my Pokémon Shuffle gaming experience.

I created a webtool and a guide to ease the process of patching the game file .cia and the save data file. It is aimed towards players playing on emulator.

I can't post links yet, but you can find the webtool on my GitHub (RainingChain) in the repo PokemonShuffleSpecialStagesDLC.

Thanks,
RainingChain

Thank you for this, this makes my life a lot easier! I'll have to reach out to you whenever I get around to actually finishing it's final update so you can update your patcher. (That's a while off though unfortunately, I have a lot otg at the moment.)

 

[alexanderjames]

Since Pokemon Shuffle 3DS is a primarily offline game which still requires going online once a day to obtain check in
rewards, and more importantly obtain a few of the Megas in the game, I have made a mod which both moves all files in the Extra Data to the base game, for those of you who haven't downloaded the extra data before they shut off the servers, and for everyone, makes the Megas which were only obtainable through the competition events act like boss stages instead of competition stages. These boss stages give the proper mega stone, a level up if you already had the stone, but regardless also give a jewel and 25 hearts. Additionally, Drop Rate Increase has been ported from Mobile, Galvantula (and temporarily Exploud) have been removed from the Survival Mode pool, the Vivillon sprite bug and the Shiny Genesect special enemy graphics bug have been patched.

You will need a Hex editor such as HxD, Flips (or presumably other patching software, flips is the one I usually use), and a decrypted copy of the Pokemon Shuffle.cia file (either dump it yourself, or go through some other means)

Spoiler: For those of you with existing save data

Installation is slightly more complicated then I'd like, but the first thing to do is back up your save file and extra data using either checkpoint or preferably JKSV, as I've seen installing a new .cia over the base game delete the save data, and you'll need to do a hex edit to your save file anyways if you want to keep it. Also back up your extra data, because you will be deleting it in order for the mod to run properly, and if you want to return to vanilla, you will need access to the extra data.

To delete the extra data after backing it up go into your system settings. Once there, go to Data Management, click 3DS, then Extra Data. You'll want to locate Pokemon Shuffle's Extra Data and delete it. What this does is prevents the extra data files from overwriting the modded files in the base game, as extra data files have some sort of verification on them that prevents me from just modding those. All relevant data from the extra data has been ported over to the mod.

Unfortunately, because I've not figured out a way to deal with code edits for 3DS games that doesn't intimidate me, there's instead a small hex edit to any existing save files which have had specials unlocked. Once you have a back up of your save file, put your SD card into your PC, make a copy of the folder the back up is in, put it somewhere safe, and then drag the one you'll be using for the preservation mod into HxD or your hex editor of choice. Basically, these values that are highlighted in the save data need to be changed to 00 00. Once you're done that, save the edits and delete the .bak file it created.

View attachment 446019

Spoiler: For those who DON'T have a save file already or don't care about theirs and want to reset

If you don't have a save file or want a fresh start and are just gonna delete yours, you'll instead be using the save file included with the mod as this one already has specials unlocked, which unfortunately doesn't happen naturally in the game. However, if you don't have a save file, you instead will want to ensure that you nullify the offset of your console through the Luma menu, as the save file will only have specials unlocked if played on a console with an offset of 0. Hopefully in the future, I want to instead make the game just always have specials available without having to worry about this.

Regardless of if you have save data or not, you'll want to patch your .cia file using Flips or whatever patching software you're using. Once you've got it downloaded its pretty easy to patch the file, you just click apply patch and follow the instructions. You have the option to either put the patched .cia file onto your SD card to be installed through FBI, or if you'd prefer to use layeredFS, you can extract the files and put the A4700000, B6680000, and all files which begin with F05 into the folder used for layeredfs. These are the only files changed in this patch, there should be 9 files which begin with F05.

Once this is all done, you should have the game load as version 1.5.0 as opposed to the usual 1.5.11, and upon clicking start, you should be getting a "Attention this game isn't up to date" message, however Special stages should be unlocked. If this is what you see, you're all good to go, the mod is working properly. For anyone using the included save file, Specials can act pretty glitchy before stage 11, or at least stage 6, so I'd suggest not playing them until you've progressed at least that far into the game.

If there are any problems, concerns, or bugs, please reach out so I can either patch them if needed or try to help with anything else related to the mod.

Special Thanks to the people who were involved in figuring out how Shuffle's files worked and datamined the game, for enabling me to create this mod, and to any other member of the community who has contributed anything for the game, you're all awesome!

EDIT: 1.2 is now available, replacing 1.1 on this post, there is also now an alternate patch which addresses SOME but not all of the versions floating around, please make sure your .cia is around 91000kb as the smaller ones floating around will not work for the moment. And make sure that your decrypted .cia file is actually output as a .cia file.

Changelog:
- Victini has RML drops after being caught, but can no longer use jewels to get more attempts, to make up for the now missing comp RMLs until I find a better solution.

- Galvantula Survival Mode patch is fixed and Exploud returns to Survival Mode.

KNOWN BUG:
- Beating a comp boss stage with 99 hearts doesn't give you the stage rewards and then bugs out as if its already given them to you.
- Stages 1-11 give the wrong initial clear rewards, this will be fixed next update.
- Nihilego does not give 5 Exp Booster Ls when defeated as its supposed to.

Not to sound like a total noob , but I’ve been having trouble getting the patch to apply properly. I’m using Flips v1.31 and trying to patch a .cia version of Pokémon Shuffle, but I keep getting the error: “This patch is not intended for this ROM.”


I’ve tried multiple ROM versions (both encrypted and decrypted), but no luck so far . Is there a specific revision of the Pokémon Shuffle ROM that the patch is meant for? Would really appreciate any guidance!

 

[Z_Tetriminos]

Not to sound like a total noob , but I’ve been having trouble getting the patch to apply properly. I’m using Flips v1.31 and trying to patch a .cia version of Pokémon Shuffle, but I keep getting the error: “This patch is not intended for this ROM.”


I’ve tried multiple ROM versions (both encrypted and decrypted), but no luck so far . Is there a specific revision of the Pokémon Shuffle ROM that the patch is meant for? Would really appreciate any guidance!

Did you try what I mentioned here?

ROM Hack  Post in thread 'Pokemon Shuffle Preservation Mod v1.1'

May 2, 2023

Can confirm it only works if you make a cia standard dump from your own 3DS with godmode9 and patch it. I tried with 3 different backups I found online and no one worked.

But your hack is functional, and that's what matters! Thanks!

• Z_Tetriminos

• 

I've recently used the same approach to install the rom in a second 3DS and it worked as well, I imported the save file from the first 2DS and it worked too, I didn't have to edit anything.

 

[OutrageousGoat]

Realizing this is a necro post, but does anyone have a line on an working copy of Shuffle for 3ds that will accept this mod or one thats already been modded? I cant find a single one anywhere that works.

Post automatically merged: Nov 4, 2025

Realizing this is a necro post, but does anyone have a line on an working copy of Shuffle for 3ds that will accept this mod or one thats already been modded? I cant find a single one anywhere that works.

 

[Mitchell03]

does anyone know how to make the data separate from the rom file?

 

[replaymikey]

does anyone know how to make the data separate from the rom file?

here's the mod for use with layeredfs

 

[celticjordan]

Greetings, everyone. I managed to get the patch working, but I was wondering if any of you has figured out a way to keep the Special Stages access AND modify the save so you have as many hearts as you want (I hate the energy mechanic). I've tried to use the events in pokemoncompletion(dot)com and use the save file downloaded from there, but the Special stage access is lost.

Should the question not be considered appropriate, please say so, and I'll delete the post. Just trying to enjoy the game with no heart limitation.

 

[SaltedNeos]

Greetings, everyone. I managed to get the patch working, but I was wondering if any of you has figured out a way to keep the Special Stages access AND modify the save so you have as many hearts as you want (I hate the energy mechanic). I've tried to use the events in pokemoncompletion(dot)com and use the save file downloaded from there, but the Special stage access is lost.

Should the question not be considered appropriate, please say so, and I'll delete the post. Just trying to enjoy the game with no heart limitation.

I actually did figure that out while I was making the patch, but I never released it and lost the files for it. I didn't make it a save edit, but edited the special shop to have 7 nhn24s for free, it was intended to make speedruns for the game possible. Realistically speaking, just editing for hearts isn't that hard if you were to just download PSSE. The save should be editable the same as any normal save file.

 

[celticjordan]

Oh, I hadn't learnt about PSSE before your reply, will definitely try it afterwards when I get back to my PC. Thank you kindly for the prompt response, and for the effort you and the team went through to preserve this game :3

 

[moonlight_rose]

Hello, does this mod make the Check In feature work again, or does it just unlock the Special Stages menu? I downloaded the mod and followed the instructions, but when I press Check In I get error code 022-2472 (failed to retrieve data for check in).

 

[celticjordan]

Hello, does this mod make the Check In feature work again, or does it just unlock the Special Stages menu? I downloaded the mod and followed the instructions, but when I press Check In I get error code 022-2472 (failed to retrieve data for check in).

Afaik it grants access directly to the Special stages, no need to Check in

 

[celticjordan]

Hi to everyone once again, after playing for a while, I changed the date in my console, and the Special stages are gone altogether, the button to access them is completely gone. I made sure the two bits shown in the guide within the savefile are set to 0, but still, no special stages. How can I fix this?

Post automatically merged: Jan 17, 2026

Hi to everyone once again, after playing for a while, I changed the date in my console, and the Special stages are gone altogether, the button to access them is completely gone. I made sure the two bits shown in the guide within the savefile are set to 0, but still, no special stages. How can I fix this?

furthermore, the unique store button is also gone

 

[Z_Tetriminos]

Hi to everyone once again, after playing for a while, I changed the date in my console, and the Special stages are gone altogether, the button to access them is completely gone. I made sure the two bits shown in the guide within the savefile are set to 0, but still, no special stages. How can I fix this?

Post automatically merged: Jan 17, 2026

furthermore, the unique store button is also gone

If I recall correctly, this would happen in the game even when it was being actively supported. It's a measure to prevent people from changing their 3DS internal date to exploit special stages and daily bonuses. Someone has posted a fix already:

you've nullified your consoles offset before, try nullifying it again.. If you've homebrewed your system, theres a good chance you've done it before. Its in the Rosalina menu. Whenever I get a bit less busy I'm hoping to make a version of the mod where this lockout can't happen at all.