Iroquois was made the flagship of Maritime Operations Group 1. In the late 1990s, Iroquois became the first warship of Maritime Forces to integrate women into the crew. On 21 March 2000, the destroyer was sent to aid the bulk carrier Leader L which had sunk northeast of Bermuda. Iroquois rescued thirteen survivors and the remains of six others. After the September 11 attacks on the United States by terrorists, Iroquois, which was at sea operating off eastern North America, was used to track aircraft entering North American airspace for NORAD. Operation Apollo was created to support the United States invasion of Afghanistan. A naval task group was formed, which Iroquois was made flagship of on 17 October. The task group was composed of Iroquois, the auxiliary vessel and frigates and . All the ships with the exception of Halifax sailed from Halifax on 24 October. Iroquois, Charlottetown and Preserver arrived in theatre on 20 November. Iroquois was later incorporated into a US amphibious ready group for escort duties for United States Marine Corps transports positioned close to Pakistan. The destroyer returned to Halifax on 27 April 2002. After the US invaded Iraq in 2003, Commodore Roger Girouard was given command of Task Force 151, comprising ships of allied nations who chose not to join the Iraq War but continued to support the War in Afghanistan. was the next Canadian ship slated to deploy to the theatre. However, Commodore Girouard requested Iroquois be sent instead, due to the vessel's flagship accommodations and better communications equipment. In order to accommodate the request, MARLANT reassigned Frederictons helicopter and aircrew to Iroquois, allowing the destroyer to sail on 24 February. However, on 27 February, the Sea King crashed into the ship's deck, forcing Iroquois to return to Halifax. The destroyer sailed with Fredericton on 5 March bound for the Persian Gulf, this time with no helicopter. Iroquois departed the theatre in June. In August 2006, the destroyer was assigned to Standing NATO Maritime Group 1 as flagship. In 2008 Iroquois, and were deployed to the waters off Somalia as part of CTF 150, the multi-national task force that concerned itself with drug and people smuggling and piracy in the region. In 2012, Iroquois was among the Canadian warships sent to the Caribbean Sea to help stem the flow of illegal drugs into North America as part of Operation Caribbe. After rust was found