Yorktown received the Atlantic Fleet's "Top Gun" award for outstanding Naval Gun Fire Support (NGFS) in 1987. During the second deployment from September 1987 to March 1988, Yorktown participated in numerous U.S. and NATO exercises, as well as multi- national exercises with Morocco, France, West Germany, Tunisia, and Turkey. It was on this Mediterranean deployment that Yorktown gained worldwide publicity from operations conducted in the Black Sea as part of Freedom of Navigation program. On February 12, 1988, while exercising the "right of innocent passage" through Soviet-claimed territorial waters (a transit which, from an operational standpoint, was not necessary), a Soviet warship "Bezzavetniy" ("Беззаветный", project 1135) intentionally collided with Yorktown in what some observers have called "the last incident of the Cold War."
In 1991, Yorktown was awarded the coveted "Old Crow's" award for Electronic Warfare excellence. In 1992 Yorktown was honored with the Marjorie Sterrett Battleship Fund Award for superb, sustained combat readiness.
Yorktown served as a stabilizing force during her third and fourth Mediterranean deployments as the world watched the end of the Cold War and the tremendous coalition victory in Operation Desert Storm. During the latter of these two deployments Yorktown participated in the first U.S. military exercises with the Romanian and Bulgarian navies, and played a key role in Operation Provide Comfort, which provided humanitarian relief and security for the Kurdish refugees in northern Iraq. In the summer of 1992, Yorktown participated in BALTOPS '92. During this cruise, Yorktown made a highly acclaimed port visit to Severomorsk, Russia, becoming the first U.S. ship to visit that port since the end of World War II.
In 1993, Yorktown was awarded the Commander, Naval Surface Forces, Atlantic Ship Safety Award for a superior safety record. Yorktown has also been awarded two Navy Unit Commendations and a Meritorious Unit Commendation, and is a four-time winner of the coveted Battle Efficiency "E".
Yorktown served as Flagship for Commander, Task Group 4.1, during Counter-Drug Operations in the Caribbean in May - July 1993. In August 1993, Yorktown participated in the joint military Exercise Solid Stance in the North Atlantic. Yorktown's operations through the end of 1993 included an October - November excursion to the Caribbean to support the United Nations embargo of Haiti. In April - May 1994, Yorktown returned to the Caribbean as Force Air Warfare Commander during joint Exercise Agile Provider. While in the Caribbean, Yorktown served as Flagship for Commander, Destroyer Squadron Six, coordinating a six ship, twenty-six missile exercise. In the Summer of 1994, Yorktown achieved a resounding score of 101 during Naval Gun Fire Support (NGFS) qualification.
In August 1994, Yorktown set sail for the Adriatic Sea as Flagship for Commander, Standing Naval Forces Atlantic in support of United Nations embargo of the Federal Republic of Yugoslavia. During this six month deployment, Yorktown served as the Air Warfare Commander for the Adriatic Sea, participating in a joint task force of ships from the United States and eight European nations. In May - June 1995, Yorktown proceeded south to serve as Air Warfare Commander for the Caribbean Sea in support of Counter-Drug Operations.
In December 1995, the Smart Ship Project Office was created and USS Yorktown was chosen as the prototype Smart Ship. The Smart Ship Program aims at reducing manning while maintaining readiness through technological installations and philosophy changes. The core technologies installed in Yorktown are a 16 workstation fiber optic Local Area Network (LAN), Integrated Bridge System (IBS), Voyage Management System (VMS), Damage Control System (DCS), Integrated Conditioning and Assessment System (ICAS), HYDRA wireless communication system, and Standard Machinery Control System (SMCS).
In May 1997, Yorktown (with a reduced crew aboard) completed a five month Counter Narcotic deployment in the Caribbean followed by test operations with and her carrier battle group. During these periods Navy Manpower and Analysis Center (NAVMAC) conducted a detailed review of manpower requirements, and Operational Test and Evaluation Force (OPTEVFOR) verified the ship's ability to meet all Required Operational Capabilities in the Projected Operating Environment (ROC/POE) doctrine for Ticonderoga-class cruisers.
On 25 September 1999 Yorktown departed Pascagoula for a four month Counter Narcotics Deployment in the Caribbean. Before beginning patrolling efforts, Yorktown embarked staff members from COMSECONDFLT. Supported by the helicopter detachment, the Second Fleet staff surveyed and photographed another island slated as a potential replacement for training exercises if the Navy is unable to continue at Vieques Island, Puerto Rico. The ship made port calls in Jamaica; Aruba; Cartagena, Colombia; Rodman, Panama; Manta, Ecuador; and Cozumel, Mexico.
In 2000, the ship underwent a dry dock maintenance overhaul in Mobile, Alabama.
As of late 2001, and since commissioning, USS Yorktown had completed five, highly successful Mediterranean deployments. The cruiser was last homeported in Pascagoula, Mississippi. Yorktown was decommissioned on 3 December 2004. As of 2008, Yorktown was scheduled to be dismantled in the next five years along with her sisters and . Since her decommissioning Yorktown has been berthed at the Naval Inactive Ships Maintenance Facility, Philadelphia, Penn.
In September 21, 1997 while on maneuvers off the coast of Cape Charles, Virginia, a crew member entered a zero into a database field causing a divide by zero error in the ship's Remote Data Base Manager which brought down all the machines on the network, causing the ship's propulsion system to fail.
Anthony DiGiorgio, a civilian contractor with a 26-year history of working on Navy control systems, reported in 1998 that the Yorktown had to be towed back to Norfolk Naval Station. Ron Redman, a deputy technical director with the Aegis Program Executive Office, backed this claim up, suggesting that such system failures had required Yorktown to be towed back to port several times.
In the August 3, 1998 issue of Government Computer News, a retraction by DiGiorgio was published. He claims the reporter altered his statements, and insists that he did not claim the Yorktown was towed into Norfolk. GCN stands by their story.
However Vice Admiral Henry Griffin denied this, reporting that Yorktown was "dead in the water" for just 2 hours and 45 minutes. Captain Richard Rushton, commanding officer of Yorktown at the time of the incident, also denied that the ship had to be towed back to port, stating that the ship returned under its own power.