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I don't know what the problem with his scripts is :/ I had issues using those as well. It should work if you use GC Rebuilder with the files I just posted.
my umbrella goes directly to Bankai
okay. i'll use the long method.

the files you posted go in the same place as the other files after ripping, right?
Yeah, they go in the &&systemdata folder after ripping.
so just to be clear, you do delete the default.dol in the root before rebuilding right
No. Leave default.dol.
Anywhere, everywhere
I should be able to look at it tomorrow on the Wii. I used GC Iso Tools because it allows for running from the command line, where you have to use the GUI in GC Rebuilder I think.
my umbrella goes directly to Bankai
oh yeah.

now i got a working iso!!!
can't i just cut the extracted folders out of the root, keep them somewhere else then rebuild. that way it'll rebuild faster while also making it so you don't have to create them again?
Edit history:
Aruki: 2014-06-22 05:17:57 am
Aruki: 2014-06-22 05:17:37 am
Yeah, you can do that if you want, t3. If you use the game.toc in the rar I posted on the last page I think it should work so you don't even need to do that, though.

reka, if you can get that working, that might be better than my method. Wish I could change the attachment in the first post so I can update the instructions/included files, heh. (Can mods do that?)
Edit history:
UchihaSasuke: 2014-06-22 05:20:04 am
my umbrella goes directly to Bankai
i used the files that parax posted and the rebuild went fast without taking away any files.

btw, once i've done the process one time, for new ones i just need to start from the randomization step, right?
yep. Once you have the files unpacked and the stuff in &&systemdata fixed you should be able to just run the randomizer again immediately, then just repack and rebuild.

By the way, if anyone's still having trouble and wants to run this on Dolphin, there's something in the readme that says how to get Dolphin to read files straight out of the game folder. That lets you skip having to rebuild the ISO, so you can just rip the files off the ISO using Dolphin, run the randomizer, and then run the .dol file directly without needing to mess with GC Rebuilder.
Anywhere, everywhere
What's annoying is that GC Rebuilder and GC ISO Tools have completely different folder hierarchies.

GC Rebuilder has "root" -> "&&systemdata", "Audio", and "Video"
GC ISO Tools has "root" and "sys". The files in &&systemdata and sys are different as well. Those programs are not compatible at all with one another it seems. Your guys' program was likely written based on the GC Rebuilder hierarchy, so that's why the script doesn't work.
Our programs don't touch any of the system data folders, they only work directly with Metroid Prime's .paks and files extracted from them.
Edit history:
UchihaSasuke: 2014-06-22 05:39:28 am
my umbrella goes directly to Bankai
i noticed that too since the filesystems weren't the same. the way dolphin ripped it was different from those 2 too since some files were in other places.

better add a note that you must use GC Rebuilder when doing this and not combine rippers/builders (i made this mistake at the start. ripped with dolphin and then tried to rebuild with GC Rebuilder and that's why i got dead isos at first)

one little thing i added was an extra .bat for the randomization step since i didn't understand how to make that step work.
Edit history:
Aruki: 2014-06-22 05:41:36 am
I added some stuff to the first post clarifying that. Unfortunately Taiga forum won't let me update the attachment so I can't update the readme included with the randomizer itself.

Sorry it's been such a pain getting this working correctly :/ I really hope we can smooth out this process in the future.
got it to work in dolphin.

couldn't get gc rebuilder to rebuild unless the "do not use game.toc" was checked and the extracted folders were cut out of the root.

how do you make the game start from the end of the frigate?
That requires a little bit of hex editing. Open Metroid1.pak and search for:

FF FF FF FF FF FF FF EB

Change the last byte from EB to E4.
do you need to use a separate memory card or something in dolphin? when i try to load an existing save the game crashes.
Uhh, I think after the game initially saves to the memory card you can go into Dolphin's memory card manager (under the Tools menu) and set it to use whatever .gci save file you want. It's been a while since I've done that so I'm not sure how it works exactly but I don't think it'll be too hard to get it working.

Actually in-game though, don't use an existing file, start a new one. The randomizer has to mess with how the game loads and saves files to get the Phazon Suit scan to work, and that's gonna cause some weird issues if the file was created on a vanilla ISO.
what do i open metroid1.pak in?
Any hex editor. I use HxD. (If you use that, it automatically creates a .bak backup file when you save it, so you'll want to either turn that off or delete the backup.)
Anywhere, everywhere
Ok, it works on Dolphin! I'll patch up the script tomorrow just to make things a little more user friendly.
it's supposed to send you to the end of the frigate after the "unidentified distress beacon..." message right? or is it after the opening cutscene?
Edit history:
Aruki: 2014-06-22 06:42:54 am
Yeah, it should place you directly at the end after that message runs.

Did you start a new file after you updated Metroid1.pak? If you're reloading an existing one, even if it says "Space Pirate Frigate 0:00", it won't work correctly.
i changed the one byte in metroid1.pak, rebuild the iso, and started from a fresh memory card entirely. ugh.