Ruby Genseki

I'm not sure but I think the partner Pokemon are loaded from the ROM rather than from the save, just like enemy Pokemon. I don't know what is written to the save when saving between battles though.

Getting them out of Citra's RAM might be the only way.

Be sure to use an older build of Citra (I use a January build) since you can't access Citra's RAM with HxD in current builds.

For questions just ask.

Well, I'm currently using a recent Citra build to play PSMD, but until a few days ago I was using a December 2016 build, I can switch back to that one if necessary.

I do have HxD, but all I've used it for was removing the outlines, so, if you could tell me how to find that specific Kommo-o's data on it, I'd gladly look for it.

Though, if trying to explain it is too much of a hassle, I could upload the ROM I'm using to Mega for you.

Please don't upload ROMs (I already have it anyway), I try to explain. I'm just bad at explaining.... xD

First of all you have to know the PID of the first Pokemon you registered for the battle.

Once you are in the battle against Kommo-o open Citra's RAM in HxD by going to Extras > Open RAM and select Citra from the list that pops up.

Now you have to search for your Pokemon's PID (I still haven't found an easier way to find the offset). Press Ctrl + F, set the datatype to Hex values and enter the PID in reversed byte order. So if it is 12345678 in PKHeX you have to search for 78563412 in HxD.

You will find it multiple times in the RAM. Go to the second hit.
At this offset you will see your first Pokemon in encrypted format. Right click in front of the PID choose Select block and set the length to 1600. Now you have marked your's and your oponent's party. Copy this into a new file.

Now from this new file you can extract the Pokemon from you oponent's party. The exact location of Kommo-o is depending on where it is in the party. Your oponent's first Pokemon is at offset 0xBA4, the second is at 0xD88 and the third at 0xF6C. Anything that looks like "00 00 00 00 00 00 ?? ?? 00 00 7E E9 71 52 B0 31" is just a placeholder/empty party slot. They are used for partner Pokemon in double battles iirc.

Now right click on the byte at 0xBA4, 0xD88 or 0xF6C, select block, set the length to E8 and save it to a new file.