1990s and 2000s
In November 1990, Bunker Hill sailed in support of Operation Desert Shield and Operation Desert Storm and served as the multinational Air Warfare Commander (AAWC) and as one of the first ships to launch a Tomahawk Land Attack Cruise Missile against Iraqi targets. Following the conclusion of the Persian Gulf War, Bunker Hill participated in organizing and establishing Operation Southern Watch, the complex enforcement of the United Nations established no-fly zone over southern Iraq. Bunker Hill made a historical visit to the Russian city Vladivostok in 1993, and then one year later she made a port visit to Qingdao in the People's Republic of China.
In March 1996, during the Third Taiwan Strait Crisis, she took station south of Taiwan to monitor missile tests by the People's Liberation Army.
In July 1998, Bunker Hill's homeport was shifted from Yokosuka, Japan back to San Diego. In Late 2000, Bunker Hill deployed with the USS Abraham Lincoln (CVN-72) Battle Group. She again participated in Operation Southern Watch and conducted boardings and inspections of over 40 merchant vessels in support of United Nations sanctions against Iraq. Bunker Hill also escorted the USS Tarawa (LHA-1) Amphibious Ready Group while conducting humanitarian operations off East Timor and training exercises in Kuwait. Bunker Hill acted as Air Defense Commander for the ARG where she designed and implemented innovative procedures for CG integration into an Amphibious Ready Group. Following the attack on USS Cole (DDG-67), Bunker Hill sortied from Bahrain to provide support and protection to seven USN and USNS ships based there and subsequently remained at sea for 67 consecutive days. Bunker Hill returned from deployment in February 2001.
Since her commissioning, Bunker Hill has deployed six times to the Persian Gulf and has earned fifteen Battle "E" Awards, including the Golden Battle "E" in 1996 and 2006 which is given when a ship receives five such awards consecutively.
In March 2006, it was announced that Lockheed Martin will upgrade the Aegis system on 22 navy vessels; the Bunker Hill is the first slated to receive the upgrade.
In March 2003 Bunker Hill was assigned to Cruiser-Destroyer Group 3.
In January 2007, the Bunker Hill was sent to the coast of Somalia to conduct antiterrorist operations as part of the USS Dwight D. Eisenhower (CVN-69) task force. She was awarded the Meritorious Unit Citation for this role.
On 28 February 2008, Bunker Hill was awarded the 2007 Battle "E" award, her 6th consecutive Battle "E".
From 1 October 2009, Bunker Hill was assigned to Carrier Strike Group One, whose flagship was the USS Carl Vinson.
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