Well it seems Ruby Weapon spawned itself for me. It wasn't there the day before. I slept, went to work, came back, ran the game, and there it was. I have no clue how this happened.
Anyways after killing the randomly spawning bastard, I looked around the savefile a bit and here's what I've found for those who cares.
On offset 0x0C1F (not including header data)
Before Ruby's Death: 05h
After Ruby's Death: 0Dh
Changing the bit back to 05h makes Ruby weapon alive again. However instead of hiding under the sand, it is now standing on top of the sand. (and waving its arms at absolutely nothing and hopefully scaring the hell out of everyone in the golden saucer =D)
*edit:
05h: both emerald and ruby are alive
0Dh: ruby is dead, emerald is alive
1Dh: both emerald and ruby are dead
my guess is:
number & 8t = ruby's death
number & 16t = emerald's death
and ultimate weapon's status is probably either &1 or &4
Here's a list of other things that changed:
Offset Before After
0xEA6 03 60 01 80 23 02
0xF2B 11 31
0xF58 7C 61
0xF84 xx xx E9 xx xx xx xx xx C2 CC E9 A2 21 67 F6 F8
0xFA3 xx 65
xx = this value changes just from re-saving. Re-saving being loading the file and saving it in a different file without doing anything ingame.
If a value changed from re-saving both before and after Ruby's death, I did not record it. There was quite a few of those.
Also I noticed that 0x0F84 is where the coordinates of Ultimate Weapon is supose to be. I haven't tried decoding the coordinates and don't know why it's changing or if the changes are significant in any way.
On the other hand, I'm still dead stuck on the Battle Square problem. Help please?