Bonanno and his ally Joe Magliocco (successor to his brother-in-law Joe Profaci) were plotting against two Commission members--Carlo Gambino and Tommy Lucchese--not the entire Commission. The Commission didn't want to start a multi-Families war by whacking Bonanno and Magliocco. The Commission wanted them to step down as Dons. Their purpose was to put in their places Dons who would be loyal to Commission members--Joe Colombo, who was allied with Carlo Gambino, and Gaspar DiGregorio, who was Stefano Magaddino's brother in law. They also aimed to break up the powerful, old-guard Castellemmare del Golfo alliance between the Bonannos and Profacis that had exerted what other Commission members resented as undue influence in the Commission.

Magliocco, terminally ill with heart disease, stepped down and paid a $55k fine. Bonanno refused. The Commission, without firing a shot, decreed he was no longer the Boss, and that DiGregorio was. That move set off a war between Bonanno members loyal to Joe, and those who wanted Gaspar. That war cost plenty of Bonanno Family lives and weakened the Family. Joe took it on the lam and finally did step down--all of this without other Commission members going to war against them. The Bonannos were no longer influential. They didn't regain their Commission seat until Joe Massino, with John Gotti's help, was seated years later.