After making a Midshipmen's cruise to South America, taking part in NATO exercises in the North Atlantic, and receiving an overhaul, "Boston" made her second Sixth Fleet tour during June–September 1958. This cruise included participation in the Lebanon crisis. During the next eight years she frequently operated in the Mediterranean, often in the role of flagship, as well as taking part in exercises off Northern Europe, in the Caribbean and off the U.S. East Coast. "Boston" served as flagship for the recovery effort of the Palomares Incident from February through April 1966.