After quite a bit of experimenting, I've successfully found a way to force the Pokémon Colosseum Japanese Bonus Disc to provide a genuine Ageto Celebi to a US (or PAL) Colosseum save file. This Celebi can then be traded to a US/PAL copy of Ruby/Sapphire/Emerald/FireRed/LeafGreen, and even migrated to the current generation of DS games.
You will need the following:
1) ISO of the Japanese Bonus Disc
2) A US or PAL copy of Pokémon Colosseum
3) US/PAL save file with all 48 Shadow Pokémon purified and an empty party slot (if you need one, use NuGaSa to restore one of these: US/PAL)
4) A US/PAL copy of a Pokémon GBA game [optional, must match the region of your Colosseum game disc]
5) A good hex editor and an understanding of how they work (HxD is recommended if you need one, Google it.)
6) A way to run Gamecube backups on your GC/Wii.
Now that you have your materials together, follow these instructions carefully.
Step 1: Open your Japanese Bonus Disc ISO in your hex editor of choice.
Step 2: Replace the following hex offsets with the capital letter 'E' (or 'P' if you have a PAL copy of Colosseum): 29AB8003, 29F4FEBB, 29F50AC3.
Step 3: Save the hacked ISO and run it with whatever backup-running method you use. Your Colosseum memory card should be in Slot A, and should have at least one party slot free in-game.
Step 4: Press A to proceed through the menus until you arrive at a screen with two options. The Shrine should be the right option, select it. A cutscene will play featuring Celebi, and you'll be told in Japanese that Celebi is now in your Colosseum party!
Step 5: Start up Colosseum and check your party. You should have a genuine Ageto Celebi!
Step 6 (optional): Transfer Celebi to Ruby/Sapphire/Emerald/FireRed/LeafGreen as you would any other Pokémon. You can also Pal Park it to the DS games after doing so.
Enjoy!
=================
After receiving your first Celebi in your Colosseum file, revisiting the Shrine in the bonus disc will reveal that you have the option to send up to 48(!) Celebi to copies of Ruby/Sapphire (one per game cart). However, this will require additional hacking to work, which can be stacked with the above in order to have a hack that works in both cases. Please note that this is UNCONFIRMED, and may damage your GBA save file! If you would prefer a safe alternative, just delete your Colosseum save that you used in the previous step and replace it with one of the ones I provided. It will forget that you had your first Celebi, and you can do that as much as you need.
Step 1: Open the ISO in a hex editor again.
Step 2: Go to the following address in hex: 2A1294A0.
Here, you'll see that there are two four-letter game IDs. By default, these are "AXPJ" (Japanese Sapphire) and "AXVJ" (Japanese Ruby). These two games are the only games that Celebi can be sent to normally. In theory, you could replace these IDs with the IDs of any Pokemon GBA games -- however, it's probably not going to work with anything but other regions of Sapphire/Ruby. That being said, replace both four-letter IDs with the following, depending on the region of the GBA game(s) you want to transfer to:
English/USA: AXPEAXVE
PAL: AXPPAXVP
Step 3: After making that replacement, save and run the hacked ISO.
Step 4: Go to the Shrine button and answer the first choice to Eagun's question. A GBA connection prompt will come up. Connect a GBA with the GBA-GCN link cable to controller slot 2, and power the game on. Make sure you've saved inside the Pokémon Center on the GBA game, and that you have at least one free party slot.
Step 5: The Celebi should be transferred, and you will be prompted (in Japanese) to turn off the GBA's power. Check your party in-game, you should have an Ageto Celebi!
Please note that the above part about the 48 Celebi hack is UNCONFIRMED, but there's no reason in theory why it wouldn't work out. I'm not responsible if your game gets screwed up.
Edit 1: Confirmed that it can be traded to Emerald/FireRed/LeafGreen, too.
Edit 2: Added (UNTESTED but theoretically working) instructions for hacking the 48 Celebi transfers into working.
Edit 3: Safe alternative to the 48 Celebi transfers until it can be confirmed.
Edit 4: Save files updated to work a little better. Don't ask.
You will need the following:
1) ISO of the Japanese Bonus Disc
2) A US or PAL copy of Pokémon Colosseum
3) US/PAL save file with all 48 Shadow Pokémon purified and an empty party slot (if you need one, use NuGaSa to restore one of these: US/PAL)
4) A US/PAL copy of a Pokémon GBA game [optional, must match the region of your Colosseum game disc]
5) A good hex editor and an understanding of how they work (HxD is recommended if you need one, Google it.)
6) A way to run Gamecube backups on your GC/Wii.
Now that you have your materials together, follow these instructions carefully.
Step 1: Open your Japanese Bonus Disc ISO in your hex editor of choice.
Step 2: Replace the following hex offsets with the capital letter 'E' (or 'P' if you have a PAL copy of Colosseum): 29AB8003, 29F4FEBB, 29F50AC3.
Step 3: Save the hacked ISO and run it with whatever backup-running method you use. Your Colosseum memory card should be in Slot A, and should have at least one party slot free in-game.
Step 4: Press A to proceed through the menus until you arrive at a screen with two options. The Shrine should be the right option, select it. A cutscene will play featuring Celebi, and you'll be told in Japanese that Celebi is now in your Colosseum party!
Step 5: Start up Colosseum and check your party. You should have a genuine Ageto Celebi!
Step 6 (optional): Transfer Celebi to Ruby/Sapphire/Emerald/FireRed/LeafGreen as you would any other Pokémon. You can also Pal Park it to the DS games after doing so.
Enjoy!
=================
After receiving your first Celebi in your Colosseum file, revisiting the Shrine in the bonus disc will reveal that you have the option to send up to 48(!) Celebi to copies of Ruby/Sapphire (one per game cart). However, this will require additional hacking to work, which can be stacked with the above in order to have a hack that works in both cases. Please note that this is UNCONFIRMED, and may damage your GBA save file! If you would prefer a safe alternative, just delete your Colosseum save that you used in the previous step and replace it with one of the ones I provided. It will forget that you had your first Celebi, and you can do that as much as you need.
Step 1: Open the ISO in a hex editor again.
Step 2: Go to the following address in hex: 2A1294A0.
Here, you'll see that there are two four-letter game IDs. By default, these are "AXPJ" (Japanese Sapphire) and "AXVJ" (Japanese Ruby). These two games are the only games that Celebi can be sent to normally. In theory, you could replace these IDs with the IDs of any Pokemon GBA games -- however, it's probably not going to work with anything but other regions of Sapphire/Ruby. That being said, replace both four-letter IDs with the following, depending on the region of the GBA game(s) you want to transfer to:
English/USA: AXPEAXVE
PAL: AXPPAXVP
Step 3: After making that replacement, save and run the hacked ISO.
Step 4: Go to the Shrine button and answer the first choice to Eagun's question. A GBA connection prompt will come up. Connect a GBA with the GBA-GCN link cable to controller slot 2, and power the game on. Make sure you've saved inside the Pokémon Center on the GBA game, and that you have at least one free party slot.
Step 5: The Celebi should be transferred, and you will be prompted (in Japanese) to turn off the GBA's power. Check your party in-game, you should have an Ageto Celebi!
Please note that the above part about the 48 Celebi hack is UNCONFIRMED, but there's no reason in theory why it wouldn't work out. I'm not responsible if your game gets screwed up.
Edit 1: Confirmed that it can be traded to Emerald/FireRed/LeafGreen, too.
Edit 2: Added (UNTESTED but theoretically working) instructions for hacking the 48 Celebi transfers into working.
Edit 3: Safe alternative to the 48 Celebi transfers until it can be confirmed.
Edit 4: Save files updated to work a little better. Don't ask.
