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In the first part of 2004, Headquarters Company, 6th Marines, deployed to Bagram Airfield, Afghanistan in support of Operation Enduring Freedom under the operational title Regimental Combat Team 6. During the first part of 2004, Battalion Landing Team 1/6 deployed to Kandahar Air Base, Afghanistan in support of Operation Enduring Freedom.
In January 2007, Headquarters Company, 6th Marines, deployed in support of Operation Iraqi Freedom, under the operational title Regimental Combat Team 6. The regiment took operational control of three infantry battalions: 3rd Battalion, 2nd Marines, 2nd Battalion, 8th Marines and 1st Battalion, 24th Marines.
Additional subordinate commands include: 1st Reconnaissance Battalion, Company C, 2nd Tank Battalion, Company B, 2nd Tank Battalion, Company B, 2nd Assault Amphibian Battalion, Company C, 2nd Combat Engineer Battalion and Battery I, 3rd Battalion 12th Marines.
In Spring 2007, these units were replaced by 2nd Battalion, 6th Marines, 2nd Battalion, 7th Marines, 3rd Battalion, 6th Marines, and Company B, 2nd Tank Battalion.
In October 2007, 1st Reconnaissance Battalion was replaced by 2nd Reconnaissance Battalion.
They served in Ramadi, Iraq from January 2009 - September 2009, when they were replaced by the 1st Brigade of the 82nd Airborne Division, Advise and Assist Brigade (AAB).
6th Marines deployed in December 2011 to Afghanistan as Regimental Combat Team 6.[23] RCT-6 arrived in Afghanistan on 24 December 2011 at Camp Bastion. RCT-6 Headquarters is currently located at FOB Delaram, AFG with Marines from the unit at Combat Out Post (COP) and Patrol Bases (PB) to support subordinate commands.