Forum user Goplat looked at the differences between the two ROMs, and found that the files differed by only a few bytes here and there. These spots were where the anti-piracy code was. So, by looking at the clean ROM, he could see what those snippets of code did:
* A subroutine at address $C0A11C is the first line of defense against pirates, being called upon startup. It first checks to make sure that there's only 8 kilobytes of SRAM, the part of memory used to hold saved games. Cartridge copiers have more, so if it detects that, the game displays a screen that says, "It is a serious crime to copy video games."
* Both games also check which kind of PPU the SNES has - if it's a PAL type (used mainly by European game systems), they display the following screen:
http://starmen.net/mother2/gameinfo/antipiracy/


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