simple guide to get Metroid Prime 2 Randomizer running on Console 
(Wii with Backwards Compatibility, Wii without BC and Wii U)

by UchihaSDA

things needed

1. Homebrew Channel installed (for Wii U, you'll need a copy of SSBB to install it)
2. Metroid Prime 2 iso (rip it from the game disc using CleanRip app on homebrew channel on a BC Wii 
or use google to find it)
3. Nintendont homebrew app (http://gbatemp.net/threads/nintendont.349258/)
4. Echoes Randomizer program (found at m2k2
https://m2k2.taigaforum.com/post/echoes_randomizer.html )
5. GC Iso Tool to open the iso and edit the paks (http://www.wiibackupmanager.co.uk/gcit.html)
6. SD Card, USB Stick or HDD (SD Cards are the simplest to use so i prefer them)
5. (optional for Wii without BC or Wii U) a controller adapter or a PS3 controller and USB cable.

steps

1. install homebre channel (look up the correct method for your console)
you only need the base homebrew channel and nothing else to run the apps needed to play randomizer

2. rip your mp2 disc with CleanRip. follow the instructions provided by CleanRip to do this. 
(this should produce an iso with the name G2ME01.iso)
you'll have to use the SD Card/USB stick in this step to save the iso and then connect it to the PC to move it there.
***if you already have an iso in your PC, you can skip this step***

3. open GC Iso Tool and locate the mp2 iso with the "open Iso" option. once you open it, 
you should see the files inside it. now, go to the save button, go to extract and then 
click on "GCReEX format..." and choose a folder to save the files. it's advisable to use an easy to find location.
once you have the files saved to a folder, go to the folder called "Metroid Prime 2 Echoes [G2ME01]"
and inside there should be "root" and "sys". enter "root" and you should see several files.
the files named "Metroid1.pak" to "Metroid5.pak" should be there.
to make things much easier, you can copy those 5 pak files to a different folder in the root of
your hard drive and give the folder a very simple name (i used '1')

4. download and extract the Randomizer tool from m2k2. once you extract it, open a notepad document and
type the following: Echoes_Randomizer "....." -i
the "....." part is the path where you have the pak files saved. example: Echoes_Randomizer C:\1 -i
once you have this, save the notepad file inside the folder where the echoes randomizer executable is located and
rename it to "mp2randomizer.bat"
to run it, just right-click on it and run it as administrator. if everything was located correctly,
the program will show a window with the randomizing steps and once it ends, you'll have the paks randomized.

5. go to the folder where you had put the paks eariler (the one with the simple name such as '1') and copy all the
pak files back to the original root folder. after this, open GC Iso Tool and click on "Open Folder..." and
go to the folder called "Metroid Prime 2 Echoes [G2ME01]". once you open it, you should see the files in the program.
now, click on "save" and go to "save ISO" and click on "trimmed" and give it a name. i recommend naming it "game"
to have it ready for Nintendont. at this point, the iso is ready to be used. you could play on Dolphin right away
if you use that to play GC games

(steps from now on are for people who want to play on console)

6. set up Nintendont using the steps provided on the site where you get it. be sure to get the latest release since
older releases have some issues. these files must be located in the SD Card/USB stick/HDD you're going to use.

7. create a folder named "games" in the root of the SD Card/USB stick/HDD, inside it create a folder with
the game's name and inside that folder put the randomized iso that you made earlier. it should be named "game.iso" or 
Nintendont won't recognize it.

8. insert the SD Card/USB stick/HDD in the Wii, boot it up and enter the homebrew channel. you should see
"Nintendont" in the list of apps. click on it and once it loads, choose SD or USB (choose only the one you're using.
USB is for both USB sticks and HDDs) and then choose the game from the list. 
the first time you play, adjust the options to enable virtual memory cards for the ability to save.

at this point, the game should load and you're ready to play.

extra notes:
for Wiis without BC or Wii U, you'll need to plug a PS3 controller with an USB cable to the console. the instructions
are withink Nintendont's instructions. 
also, on Wii U, you can't plug USB devices until you're in Wii mode because the Wii U tries to format them while
in the Wii U menu.

there's also sometimes an issue with the ISO being too big for the NTSC version. it's recommendable to use the PAL
version since that issue never happens in it. if you really want to use the NTSC version, an easy way to fix the
issue is deleting a file to reduce the file size. 
you can delete a music track from mutiplayer such as "multiplay9-32-3.dsp" from the audio folder to do this.