With Joe Bonanno missing, the Commission soon lost its patience, probably figuring that they were being played by the elusive boss. They ruled that Bonanno would no longer be considered the head of his family and appointed capo Gaspar DiGregorio the new boss. (DiGregorio had his own beef with Bonanno for earlier denying him the position of family consigliere, which he felt he deserved. Instead Bonanno had appointed his own son Bill.) Family members took sides, splitting into two camps, the Bonanno loyalists led by Bill Bonanno and the Commission-backed faction led by DiGregorio.

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Harsh words soon led to armed skirmishes on the streets of New York. The other families frowned down on these public outbursts. The Banana War drew unwanted attention to the mob and was ultimately bad for everybody's business. They wanted it stopped. DiGregorio called for a sit-down to put together a peace treaty. Representatives from both sides agreed to meet at a house on Troutman Street in Brooklyn after dark. DiGregorio and his men arrived first, but compromise was not on their minds. As soon as Bill Bonanno showed up, DiGregorio's men opened fire with shotguns and rifles. Bonanno and his men retaliated, shooting into the dark at their unseen assailants. Over 100 rounds were fired, and by some miracle no one died.

Joe Bonanno then offered the Commission a deal to end the violence. He would give up his claim to the family and retire to Arizona if the Commission would accept his son Bill and brother-in-law Frank Labruzzo as boss and underboss. The Commission saw right through his offer, knowing that Joe Bonanno would remain in control even if he didn't have the title. They came back with a counter offer: Bonanno could retire with his life, but the Commission would name the next boss-DiGregorio.

The war continued. Joe Bonanno resurfaced in May 1966 - 19 months after his alleged kidnapping - then quickly dropped out of sight again. The Commission grew impatient with DiGregorio's ineffective efforts to squelch the Bonanno loyalists, so they replaced him with someone they felt could do the job, Paul Sciacca. But Bonanno's men fought like guerillas. Three of Sciacca's men were mowed down by machine-gun fire inside a Queens restaurant. The fighting escalated, and each side lost five more men.

Finally in 1968 Joe Bonanno suffered a major heart attack. He flew to Arizona and informed the Commission that he was retiring, this time for good. The Commission was naturally wary of anything Bonanno did or said, but as time passed, the shootings diminished, and the torn family eventually accepted Sciacca as their leader. He was later succeeded by Natale Evola who was succeeded by Philip "Rusty" Rastelli.

Both Joe and Bill Bonanno wrote books about their Mafia experiences. Such public disclosures were serious violations of omerta, the Mafia code of silence and especially surprising coming from these self-proclaimed "men of honor." It's generally agreed that these tomes paint a picture of the way father and son wished things had been as opposed to way they actually were. The Bonannos also cooperated with author Gay Talese for his book about the crime family, Honor Thy Father.

Jerry Capeci in The Complete Idiot's Guide to the Mafia quotes FBI agent Bill Roemer who had many dealings with Bonanno in Arizona. Roemer called Bonanno "a constant whiner" who "did not live up to the 'tradition' he speaks about so much in his book.'"

In 2002 Joe Bonanno died of natural causes in Tucson. He was 97 years old.