Back when I was a kid in the 80's. I cracked one of the Ultima games. I had it on my hard drive and didn't want to stick a floppy in every time I ran it.
The code decrypted itself, which confused debuggers, and then loaded a special sector from disk. It was a small sector buried in the payload of a larger sector, so the track was too big to copy with standard tools. The data in the sector was just the start address of the program. My fix was to change executable header to point to the correct start address.
my story of this is Atari Macro Assembler. The floppy had a specific sector that was damaged, and the loader would test this sector to ensure it was in fact damaged. this was obvious becuase whenever loading the floppy, you had to wait for one of those big "BZZT....BZZT" things where the 810 drive was trying to access a bad sector and giving up. I was able to disassemble maybe the first 30 bytes of the boot to see it checking this and doing the jmp. I just overwrote it with a single jmp and got not just a copy but much faster loading without the BZZTBZZT part.