In February 1989 the McKee performed the first at-sea weapons transfer to a submarine since WWII, to the USS Ohio (SSBN-726).
In March 1990, the McKee continued leading the way for submarine tenders by participating in the first underway fuel replenishment by a Pacific Fleet submarine tender. This fuel was in preparation for deployment to the Persian Gulf in January 1991.
In 1995, after the decommissioning of USS Dixon, McKee provided all support to San Diego based submarines. Assistance was also provided to many Allied submarines while they visited Point Loma.
In 1998, McKee earned a third Meritorious Unit Commendation following a six month deployment to Pearl Harbor. During this deployment, McKee provided services and conducted repairs to both U.S. and Allied submarines and surface combatants. Upon returning to San Diego, the ship took the lead in establishing shore-based services that will support the submarines after McKee's departure.
In November 1998 the weapons department of the USS McKee loaded Tomahawk cruise missles onto the HMS Splendid. These were the first of 67 Tomahawk cruise missles sold to the Royal Navy and the first British submarine to receive the Tomahawk missiles. They were later used by the HMS Splendid in offensive operations in Yugoslavia.
USS McKee was one of first ships to integrate female sailors and as a consequence, while unofficially was also known as the "Love Boat" by many of her crew, and the crew members of submarines, assigned to Submarine Squadron 11 for the many relationships that sprung up during the 1990s