1990s

In August 1990, Stump transited to Avondale Shipyard in New Orleans, Louisiana, for overhaul and major combat systems upgrade. She received the Vertical Launch System (VLS) for the BGM-109 Tomahawk missile. Stump also received the integrated AN/SQQ-89 USW system.

In November 1992, Stump deployed to the Persian Gulf and Northern Red Sea as part of MEF (1–93) to serve as a ready strike platform. The highlight of the deployment was the Tomahawk missile strike launched against Iraq in support of Operation Southern Watch on 17 January 1993.

In July 1994, Stump again deployed to South America for UNITAS XXXV serving as the flagship for the commander of the U.S. South Atlantic Force. Stump re-visited eight South American nations, as well as completing another transit of the Chilean inland waterway.

In February 1995, Stump deployed to the Caribbean Sea in support of counter drug operations, transiting the Panama Canal. During this period Stump participated in a search and rescue mission in the Pacific. In cooperation with a Colombian Coast Guard cutter, Stump located and recovered a survivor of a wrecked Colombian vessel. Stump returned in April 1995.

As part of a reorganization announced in mid-1995 of the Atlantic Fleet's surface combatant ships into six battle groups, nine destroyer squadrons and a new Western Hemisphere Group, Stump was reassigned to Destroyer Squadron Two. The reorganization was to be phased in over the summer and take effect on 31 August, with homeport shifts to occur through 1998.

Stump deployed in August 1996 for a Middle Eastern Force cruise to conduct maritime interception operations and act as ready strike destroyer in the Persian Gulf. Stump relieved USS Laboon on 28 September as the maritime interception operations/strike platform in the northern Persian Gulf. While in the Persian Gulf, Stump completed over 40 boardings in support of maritime interdiction operations and participated in 11 Persian Gulf Tomahawk exercises, including one as launch area coordinator. A mainstay during this deployment, Stump remained underway for over eighty percent of the time she was in the Persian Gulf.

Following the return from her Middle Eastern Force deployment in February 1997, Stump conducted an extensive dry-docking selected restricted availability and immediately commenced a training cycle which culminated in a final evaluation period. In January 1998 Stump commenced work-ups for its upcoming Sixth Fleet deployment by participating in COMPTUEX and JTFEX as part of the Eisenhower carrier battle group.

In March 1998 the Sara Ann (a fishing trawler) was operating off the Virginia Capes when the seas became too much and she started taking on water. Stump, while conducting routine operations on 17 April 1998, was informed by United States Coast Guard Station Portsmouth that the Sara Ann was in distress. Stump subsequently rescued four civilians about 65 nautical miles off Cape Hatteras, North Carolina. Stump provided safe passage back to Norfolk, Virginia.

Stump deployed to the Mediterranean as part of Sixth Fleet in June 1998. Stump, as part of Destroyer Squadron Two, joined five other nations and other U.S. Navy warships in the central Mediterranean for the execution of SHAREM 125, from 9 to 15 July 1998. SHAREM 125 was the latest in a series of SHAREM exercises designed to test and evaluate undersea warfare tactics, weapons, sensors and procedures. SHAREM is an established in 1969 to continuously improve the quality of undersea warfare.

2000s

Stump took part in the Fleet Battle Experiment Hotel (FBE-H) which was conducted by units of the U.S. 2nd Fleet and personnel of the Navy Warfare Development Command (NWDC) from 28 August to 12 September 2000 off the Virginia Capes and in the Gulf of Mexico. This was the eighth in a series of fleet battle experiments designed to evaluate new naval warfare concepts and technological capabilities. Under U.S. Joint Forces Command's overarching experiment, "Millennium Challenge 00", FBE-H ran concurrently with the U.S. Army's Joint Contingency Force Advanced Warfighting Experiment, the U.S. Air Force Joint Contingency Force Experiment 2000 and the U.S. Marine Corps' Millennium Dragon.

The focus of FBE-H was the application of network-centric operations in gaining and sustaining access in support of follow-on joint operations. Access denial was expected to be the focus of any potential adversary's strategy. Specifically, FBE-H further developed NWDC's draft Access Concept entitled "Poseidon's Presence". In addition, the NATO exercise "Unified Spirit" ran concurrently with the JTFEX, with forces from Canada, Denmark, France, Germany and the United Kingdom playing major roles.

Stump deployed in late November 2000 with the USS Harry S. Truman carrier battle group. Prior to that, Stump took part in Joint Task Force Exercise (JTFEX) 01-1, to certify the carrier battle group for deployment. This was the first deployment for Truman, which had been commissioned in 1998. The deployment included extensive operations in the Mediterranean Sea, Indian Ocean and primarily the Persian Gulf. While operating in the Persian Gulf, the Truman battle group enforced United Nations sanctions against Iraq by diverting 22 vessels with more than $5 million of suspected contraband cargo. Throughout the deployment, the battle group also participated in numerous international exercises, including Arabian Gauntlet, an 11-nation exercise that involved more than 20 ships. Additionally, U.S. sailors worked with military forces from Oman, Jordan, Tunisia, Kuwait, Bahrain and the United Arab Emirates, improving interoperability and strengthening relationships with those countries. Stump, along with the rest of the battle group ships returned home on 24 May 2001.

In mid-October 2003 Stump operated off the coast of Argentina with the frigate USS Robert G. Bradley as part of the annual UNITAS exercise which involved naval forces from Argentina, Brazil, Peru, Spain and Uruguay.

Deployments and ports of call

MED-MEF 3–88: Rota Spain, Ibiza Spain, Marseilles France, Cavaliere France, Genoa Italy, ASU Bahrain, with a brief stop for Suez Canal traffic in Port Said Egypt and a brief stop for fuel in Djibouti.