Deducted

Yes, the ekx goes in the root. As for why PKHeX exporting .ek6 only, I have no idea but if you save it under 'All Files' you should be able to save it as .ekx without the need to rename it.

Odd. So you manually deleted the injectiondebug without re-adding the code.bin file? I did it like 9 times just to make sure, and it's only worked when I've had the file. The only time it works without it is if I delete the code.bin, the injectiondebug.bin, and pokemon.ekx and re-add code.bin and pokemon.ekx and start fresh. But afterwards, the injectiondebug appears and just stays there.

Edited my post but in case if anyone might still have problems After toying with it a few more times, I advise to not delete the injectiondebug file once you've had it. If you do happen to delete it, or having the problem if not having one appear in your SD card, DELETE THE CODE.BIN FILE AND RE-ADD IT TO YOUR SD CARD. I did this multiple times and I can say it works. How do you extract the SID? I'd like to do the same to mine to figure it out and use it for genning all of my pokes.

So after 30 minutes, I got it to work. First time I tried I got a bad egg, turns out the save file was named pokemon.ekx.pk6. The next few tries, I got nothin', not even eggs. I cleared cookies/history everything. Wasn't even gettiing the debuginjection. So I ended up just completely making a new pokemon file on PKHeX, saved it as 'pokemon.ekx' under 'All Files', re-added both that and the code.bin file. I don't know if this matters since it worked for quite a bunch of people already but what I did different was... 1.) Open the game 2.) Open your boxes, switch to any box other than Box 1 3.) Go to your Home page while you're still on that box (not box 1, do not exit your boxes either) this is the only thing I tried differently and turns out it worked 4.) Open your camera and scan the QR code http://i.imgur.com/Xsv1bLx.png 5.) It's going to say failed to load things on this page but just wait, it's supposed to crash with a pop-up, just click ok 6.) Resume your game and just switch back to Box 1, and you should have it. If anything, I'm on 9.4 on a regular 3DS. As to how PKHeX works, I have no idea as I've never used it, I just picked a pokemon and saved it. Although after playing with it a few times, the only thing I'm curious is how to figure out the SID? Pretty sure I saw someone being able to read their SID from the injectiondebug file so if someone could help me out with that, that would be great. My file's right here https://mega.co.nz/#!O1kC2RAY!q7WNoA9zh3YOkvpZhiQfXj6u5Uu_wx1KQuOlyGRiUfg A question that may have been asked already, is it required to delete the injectiondebug file after each successful attempt? EDIT: After toying with it a few more times, I advise to not delete the injectiondebug file once you've had it. If you do happen to delete it, or having the problem if not having one appear in your SD card, DELETE THE CODE.BIN FILE AND RE-ADD IT TO YOUR SD CARD. I did this multiple times and I can say it works.