In 1963, Joseph Bonanno, the head of the Bonanno crime family, made plans to assassinate several rivals on the Mafia Commission—bosses Tommy Lucchese, Carlo Gambino, and Stefano Magaddino. Bonanno sought Magliocco's support, and Magliocco readily agreed. Not only was he chafing at being denied a seat on the Commission, but Bonanno and Profaci had been close allies for over 30 years prior to Profaci's death. Bonanno's audacious goal was to take over the National Crime Syndicate and make Magliocco his right hand man.[8]

Magliocco was assigned the task of killing Lucchese and Gambino, and gave the contract to one of his top hit men, Joe Colombo. However, the opportunistic Colombo revealed the plot to its targets. The other bosses quickly realized that Magliocco could not have planned this himself. Remembering how close Bonanno was with Magliocco (and before him, Profaci), as well as their close ties through marriages, the other bosses concluded Bonanno was the real mastermind.