Bonanno and Joe Profaci had been allies since both were made Dons after the Castellemmarese War of 1930-31. Following Profaci's war with the Gallos, Gambino began "suggesting" that Profaci step down as Don, but with Bonanno's support, he stayed on the Commission. After Profaci died in 1962, Joe Magliocco, his brother in law and second in command, became Don. Then Gambino openly opposed Magliocco's Donship, and encouraged factions in his family to rebel against their new boss.

In retaliation, Bonanno and Magliocco began plotting to whack Gambino and Tommy Lucchese. But the plot was ratted out to Gambino by Joe Colombo, then a captain under Magliocco. The Commission ordered Magliocco to step down, and to pay a $55,000 fine. Terminally ill with heart disease, Magliocco complied; Colombo became Don of his family. The Commission next ordered Bonanno to come in and explain himself. He refused. The Commission then declared that Bonanno no longer was Don; in his place they installed Gaspar DiGregorio, a longtime close associate of Bonnanno who had been best man at his wedding. DiGregorio also was brother in law of Stefano Magaddino, Don of Buffalo, NY, Bonannno's cousin, who had a grudge against him for "planting flags" in southern Canada. That started the famous "Banana War" that resulted in Bonanno's "kidnapping" and the dissolution of his family.