South Carolina departed 5 January 1990 for Limited Team Training in Guantanamo Bay, Cuba. The cruiser again set sail for the Caribbean on 12 March 1990 for law enforcement operations returning on 13 April 1990 having acted as Coast Guard, COMCARIBRON flagship and making two drug interdictions. South Carolina returned to the Caribbean in July for counter narcotics operations, where she served as flagship for Commander, Joint Task Group 4 and COMCARIBRON.
South Carolina departed 1 October 1990 for operations with the Saratoga Battle Group. Following a solo trans-Atlantic crossing, she transited the Suez Canal for the first time in her history. During Operation Desert Shield, she served as flagship for COMDESRON 24, the Maritime Interdiction Force Commander in the northern Red Sea. South Carolina conducted twenty-seven boardings during Maritime Interdiction Force operations. Admiral Frank Kelso, Chief of Naval Operations, visited the South Carolina on station 7 November 1990.
Upon completion of Maritime Interdiction Force operations, South Carolina was selected as the first nuclear powered warship to visit the Jeddah, Saudi Arabia. In January 1991 the South Carolina participated in operations in the Central Mediterranean with the Theodore Roosevelt and America Battle Groups.
It sortied early from Taranto, in Italy 17 January 1991 at the start of Operation Desert Storm. South Carolina acted as an Anti-Air Warfare Commander for the Mediterranean, protecting operation Silver Cloud air corridors and the approaches to the Suez Canal. South Carolina acted as on-scene commander and supervised the recovery of four survivors and 29 bodies from the sinking merchant ship Continental Lotus. South Carolina returned to homeport on 28 March 1991. South Carolina entered Norfolk Naval Shipyard for a Combat System New Threat Upgrade and refueling of both reactors and left the shipyard 30 March 1994 with a new lease on life.
Following nuclear refueling, she participated in Operation Able Vigil Forces to assist in the rescue and transport of thousands of Cuban migrants; its crew members were awarded the Coast Guard Commendation Medal.
South Carolina's first post-refueling deployment was to the Straits of Florida during October and November 1994 to rescue Cuban refugees who were fleeing their homeland in hopes of reaching the United States. South Carolina commenced workups in the spring in preparations for her next major deployment.
In the fall of 1995, she started her eleventh deployment. This cruise saw service off the coast of the former republics of Yugoslavia in support of Operations Deny Flight, Sharp Guard, and Decisive Endeavor, which was part of the overall NATO Operation Joint Endeavor. South Carolina acted as "Red Crown" and Air Warfare Commander in the Adriatic Sea, earning the NATO Medal, Meritorious Unit Commendation, and Armed Forces Service Medals. South Carolina returned to homeport in the spring of 1996. South Carolina completed all unit work-up phases and began fleet operations with the George Washington Battle Group in the spring of 1997. From April to June 1997 South Carolina conducted a COMPTUEX with the George Washington Battle Group coordinating and acting as Air Warfare Commander for the largest and most successful surface-to-air missile exercise in the Atlantic fleet. In August 1997, South Carolina participated in Fleetex and completed all preparations for deployment.
In October 1997, the cruiser began its final Mediterranean cruise visiting thirteen ports of call from Haifa, Israel to Naples, Italy and Rota, Spain. She served as the Sixth Fleet Air Warfare Commander and participated in three major NATO exercises. The ship returned to homeport Norfolk in April 1998. Just weeks after returning from the Mediterranean, South Carolina returned to sea for six weeks of Counter Narcotics operations in the South Western Caribbean.
The ship conducted its final port visit in Charleston, South Carolina between 10 August and 14 August 1998. South Carolina was deactivated on 4 September 1998 The last of the crew left in July 1999, with the exception of a small contingent to escort her through the Panama Canal and to Bremerton, WA where she entered the Nuclear Powered Ship and Submarine Recycling Program at Puget Sound Naval Shipyard on 1 October 1999. She was stricken from the Naval Vessel Register on 30 July 1999, and on 28 March 2000 ceased to exist.
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