DISCLAIMER: THIS IS AN EXTREMELY OUTDATED METHOD OF INSTALLING OOTHAX.

OOT3DHAX FOR *HAX 2.5
hooray
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Well everyone, yesterday yellows8 and smealum officially released some support for OoT3DHax with *hax 2.5, so I figure that now is a better time than ever to get a tutorial done.
This time around, there are quite a bit of ways that you can install the hax, so pick your method and get moving!

METHOD 1: SECONDARY HAX
This method is the traditional, original method, which requires another entrypoint for installation.
PLEASE NOTE: Even if you had an old version of OoT3DHax using ninjhax 2.1, you'll still need to follow ALL of the steps!

1.) Download the 'homebrew starter kit', which now includes the exploit installer.
2.) Drag the contents of the .ZIP file directly to the SD card
4.) Follow the steps to get Ironhax/Ninjhax/Menuhax/Rumblehax/WHATEVERhax working and back up your OoT3D saves. (You can use this if you'd like.)
5.) Go ahead and launch OoT3D, and as the game is booting, hold A, B, X, and Y. This will bring up a prompt asking if you want to wipe the save files. Go through with it, and wipe all save data. (Remember, this can be restored later if you want.)
6.) Exit out of OoT3D, and load your preferred exploit again. This time, run the OoT3DHax installer.
6 1/2.) Follow all of the onscreen instructions. Mostly everything should automatically detected, so just give all of the options a quick glance before progressing.
7.) If all goes well, the payload should successfully install.
8.) Restart the system and boot up OoT3D again. There should now be a savefile named 'Haxxxxxx**********...' which extends past the screen. Go ahead and start that one.
9.) Click any of the menu buttons, interact with anything, play the ocarina... basically do any action to trigger something.
10.) The Homebrew Launcher should load up, now with *hax 2.5!

DEMO VIDEO COMING SOON

METHOD 2: POWERSAVES
Here's a method using Datel's 3DS Powersave Device, which basically directly installs the save.
For the sake of not repeating things, check out Ignisflame's thread here. It pretty much covers all that you need for this method.

METHOD 3: DS FLASHING
Probably the most inconvenient way, this is still a method of getting them good old hax into OoT3D. Thank zoogie for writing up this tutorial!

Aaaaaand there you have it, ladies and gentlemen! Once OoT3DHax is installed, go on and do a little happy dance! You now have a backup entrypoint.
Happy homebrewing!

Old Tutorial:

Warning: Spoilers inside!

Hello all! So, after having a bit of trouble with getting this to work, I decided that I'd make a tutorial on how to use this for general convenience.

PLEASE NOTE: This is so far confirmed to work with 9.2 EU (only on a physical copy), 9.9 all regions, and 10.0 in all regions. I haven't seen much of any one else test this on other firmwares, so if you could, that'd be super cool. Oh, and also, I didn't create this exploit. I'm merely teaching you how to install it.

1.) Download the 'oot3dhax_installer'
2.) Drag the '3ds' folder directly to the root of your SD card to go alongside your other homebrew.
3.) Download any homebrew in a .3DSX format and place it in the installer's app folder. (it's called 'ootsdhax_installer') The file can be named anything (besides 'boot'), but for convenience, I just named it 'payload.3dsx'.
4.) Follow the steps to get TubeHax/IronHax working and back up your OoT3D saves. (You can use this.)
5.) Go ahead and launch OoT3D, and as the game is booting, hold A, B, X, and Y. This will ask you if you want to wipe the save files. Go through with it, and wipe all save data. (Remember, this can be restored later if you want.)
6.) Exit out of OoT3D, and load TubeHax/IronHax again. This time, run the OoT3DHax installer and follow all of the instructions.
7.) If all goes well, the payload should successfully install.
8.) Boot up OoT3D again. There should now be a savefile named 'idleaway**********...' which extends past the screen. Go ahead and start that one.
9.) Click any of the menu buttons, interact with anything, play the ocarina... basically do any action to trigger something.
10.) Your .3DSX should now load!

Happy homebrewing!

VIDEO TUTORIAL: