In late 2000, "Bunker Hill" deployed with the 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 Amphibious Ready Group (ARG) 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 ARG. Following the attack on the destroyer , "Bunker Hill" sortied from Bahrain to provide support and protection to seven United States Navy and United States Naval Ships (auxiliary vessels) based there and subsequently remained at sea for 67 consecutive days. "Bunker Hill" returned from deployment in February 2001.