Oh my gosh,t he wheelchair scene. It was so shocking. But I think that Cloud's lowest point is probably nearly killing Aeris. Aside from that, begging Hojo. Only because when he's in the wheelchair, it's not due to his own issues, but rather physical poisoning.

Either way, his arc is so huge and deep, he's just such a great character to dissect. ;) (Hojo thought so, too. ;D )