I think a great story is that of the Bonanno's rise and fall with Joe Bananas and their rise and fall with Joe Massino....even though Massino turned out to be a huge hypocrite and rat, the fundamental changes that he instilled in family structure will ultimately help the families in the long run.
I was thinking of the bonnanos too, but mostly focused on Massino:
One of the NY mafia families is kicked off the commission and left for dead because they were infiltrated by a federal agent and their family is largely made up of drug dealers. One capo (Massino) takes control of the family, takes them underground, changes all the rules and brings them to the top of the country's crime hierarchy. And he does all this, just to later get caught and become a rat.
