"Coontz" returned to the United States on 23 March 1962 to rejoin the U.S. First Fleet and became the flagship of the Commander, Destroyer Squadron 17 in April 1962. On the second anniversary of her awards for excellence in Operations, Engineering and Gunnery, "Coontz" flew the flag of the Commander, Cruiser-Destroyer Flotilla 11 from 1 August to 11 November 1962, when she again became the flagship for Commander, Destroyer Squadron 17. In October 1962 "Coontz" left San Diego and sailed out to sea about to provide protection for the Camp Pendleton Marine transports just in case they were needed during the Cuban Missile Crisis.