Way back in Amazing Spiderman 149 (Oct 1975), Ben Reilly was revealed as a clone of Spiderman made by the jackal( with memory implants so he thought he was the real Spiderman), in #150 Ben was killed (or so we though). Then in 1994 Web of Spider-Man #117(and Amazing #394) revealed that actually Ben had not been killed but had been roaming around the country trying to sort his life out (and also fighting Kaine- another Spiderman clone but imperfect), to cut a long story sort, when Ben come back it was revealed that Ben was the original Spiderman and peter was the clone(so what they where saying was that for the past 20 years in the comics it as been the clone not the real one Spiderman), peter went off with MJ and let Ben become Spiderman, peter lost is powers, then peter regained his powers, then after about 1 or 2 years it was revealed that after all peter was the original Spiderman and Ben was the clone they had got it wrong, Ben was killed and peter(the original Spiderman ) lived happily ever after.
There a lot more that happened in all this but that was the outline of the story