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In 1995, as part of an expansion of the number of Australian Army infantry battalions, the 2nd/4th Battalion, Royal Australian Regiment—then operating as a standard light infantry battalion—was delinked into separate battalions which resumed their original identities as the 2nd and 4th Battalions. The decision was then taken that the 4th Battalion would become a Regular Army commando unit and on 1 February 1997 the unit was renamed to 4th Battalion, Royal Australian Regiment (Commando) (4 RAR Cdo). The unit would be structured for both conventional operations and domestic counter-terrorism, with an initial establishment of a battalion headquarters, Tactical Assault Group, two commando companies, logistic support company, logistic support company, operational support company and a signal squadron. Regular serving members were given the opportunity to undertake special forces training provided by the Commando Training Wing of the Reserve 1st Commando Regiment, or elect to be posted to a conventional forces unit. No General Reserve positions existed in the new structure, and reserve members discharged or posted to reserve units.

The initial years were busy with the unit creating a structure and recruiting members suitable for commando training, while conducting sub-unit and unit training activities. B Company was raised in 1997, followed by C Company in 1999, both of which took 24 months to reach full maturity.

A small team from 4 RAR (Cdo) deployed to East Timor as part of the International Force for East Timor (INTERFET) in September 1999 providing close personal protection for the media and also as interpreters in the initial months. In 2000, elements were involved in the evacuation of Australian nationals from the Solomon Islands in June. While later that year, 4 RAR (Cdo) assisted with counter-terrorism at the Sydney Olympic Games as part of Joint Task Force 114, with C Company on standby as a response force such as providing a cordon around an incident site in support of the SASR.

4 RAR (Cdo) deployed again to East Timor as a part of the United Nations Transitional Administration in East Timor (UNTAET) in 2001. When notified to replace 1 RAR in East Timor, 4 RAR had not long previously been raised as a commando battalion, developing special forces capabilities to supplement those of the SASR. With the commitment to East Timor continuing, however, 4 RAR was re-roled as a light infantry battalion for deployment to East Timor as AUSBATT IV.

This involved reorganising from the existing two commando-companies structure to a light infantry battalion with four companies and a growth in the unit from 220 to 670 personnel. This saw B and C Company remain commando-qualified. A Company was formed in June 2000 followed by D Company in November both filled with Regular infantry soldiers posted in to the unit. The battalion took official control over Area of Operations (AO) Matilda in the northern border region on 25 April under the command of Lieutenant Colonel Jeff Sengelman.
Following the battalion's return from East Timor it was again restructured to resume its role as a two-company commando battalion. However, in 2001 the Australian Government directed the permanent establishment of a second TAG to be based on the east coast of Australia. The TAG is supplemented by clearance divers from the Navy Clearance Diving Branch who form the Water troop. A Company was subsequently raised as a commando company in 2002. Following the creation of SOCOMD in 2002 and the Bali bombings in October that year, further resources became available. The battalion was subsequently involved in security operations for the Commonwealth Heads of Government Meeting (CHOGM) in Queensland in 2002. Elements of the battalion were also involved in the boarding of a North Korean freighter, the MV Pong Su—which was suspected of drug smuggling—off Newcastle on 20 April 2003. In 2005, a fourth commando company was subsequently raised, with D Company being formed.
IRAQ (2003)
The battalion provided a commando force element as part of the Australian contribution to the 2003 invasion of Iraq, known as Operation Falconer. A reinforced commando platoon formed an element of the Australian Special Forces Task Group (SFTG), which also included 1 Squadron, SASR, a troop from the Incident Response Regiment, and three CH-47 Chinook helicopters from the 5th Aviation Regiment. The commandos formed the "quick reaction" element for the task group. The SFTG operated in western Iraq where it was successful in securing its area of operations, including the huge Al Asad Air Base. After the invasion was complete, the 40-man commando element provided security to humanitarian assistance missions and other security operations, later providing close protection for Australian officials in Baghdad as part of Operation Catalyst.
The Pong Su incident began on 16 April 2003 when heroin was smuggled from the Pong Su, a North Korean cargo ship, onto an Australian beach. Australian military special forces subsequently boarded the Pong Su in Australian territorial waters four days later. The ship was suspected of being involved in smuggling almost 125 kilograms (276 lb) of heroin into Australia with an estimated street value of A$160 million.
Later, in May 2006 a commando company group was deployed to Timor Leste as part of Operation Astute, after relations between the East Timorese government and military forces broke down. The commandos operated alongside the SASR as part of the Special Forces Component and were tasked with advanced force operations in preparation for the arrival of follow-on forces, focusing on Dili Airport. In March 2007, the commandos, along with elements of the SASR, took part in the Battle of Same during which five rebels were killed during an unsuccessful attempt to apprehend the rebel leader, Alfredo Reinado. After the battle, the commandos and SASR elements were withdrawn at the request of the East Timorese government in order to start negotiations with the rebels.

Later, the battalion was tasked with supporting the security and counter terrorism response force arrangements for the 2006 Commonwealth Games in Melbourne.
Meanwhile, in August 2005 an Australian Special Operations Task Group (SOTG) was deployed to Afghanistan as part of Operation Slipper II, operating in the southern province of Uruzgan. The SOTG, based on similar structure deployed during Operation Falconer, was made up of elements from the SASR, a commando platoon plus, and a troop from the Incident Response Regiment. Two CH-47 Chinook helicopters from the 5th Aviation Regiment were deployed to Afghanistan in March 2006 to support the SOTG. A forward operating base was subsequently established at Tarin Kowt. During this deployment the Commandos were involved in Operation Perth which resulted in the death of over 150 Taliban and al-Qaeda fighters in nine days of fierce fighting in the Chora district of Uruzgan Province. During this period the task group was on patrol for 306 days and involved in 139 contacts and sustained 11 soldiers wounded.

A 300-strong Special Operations Task Group (SOTG) was subsequently deployed to support the Reconstruction Taskforce in April 2007, including a commando company group, elements of the SASR, and an integral combat service support team. In the latter part of 2008 the commando company conducted a disruption operation in Helmand province as part of Operation Eagle's Summit, which was a major coalition operation conducted in support of the transport and installation of an additional turbine for the Kajaki Dam hydroelectric facility. In March and April 2009, SOTG killed 80 Taliban fighters in a major four-week operation in Helmand Province, without suffering any casualties. Further operations undertaken include the Battle of Gizab in April 2010, and the Shah Wali Kot Offensive in June 2010, which resulted in heavy insurgent casualties. The bulk of SOTG was withdrawn from Afghanistan in late 2013 as part of a drawdown of Australian forces, although some special forces remained after this date as part of the small Australian force maintained in the country. The Regiment lost 12 personnel killed while deployed to Afghanistan, along with one killed during a pre-deployment exercise.

The Regiment served in 20 SOTG rotations in Afghanistan, with deployments ranging from about four to six, seven, and eight months. For its actions, the Regiment was collectively awarded the Unit Citation for Gallantry and the Meritorious Unit Citation. On 26 March 2013, it was announced that Special Operations Command would receive the first battle honour awarded to an Australian Army unit for actions since the end of the Vietnam War for its performance during the Shah Wali Kot Offensive in Afghanistan from May to June 2010. The battle honour, titled "Eastern Shah Wali Kot", was awarded in recognition of the operational actions of the SASR and 2nd Commando Regiment from Australian Special Operations Task Group Rotation XII. A number of the regiment's personnel have also received individual decorations for their actions in Afghanistan. A posthumous Victoria Cross for Australia was awarded to Cameron Baird for actions in Uruzgan Province in June 2013. In addition, as of October 2010 six Distinguished Service Crosses, eleven Distinguished Service Medals, seven Medals for Gallantry and three Stars of Gallantry had been awarded to 2nd Commando Regiment personnel for service in Afghanistan.
IRAQ (2014)
In September 2014, as part of Operation Okra the Australian Army deployed a Special Operations Task Group (SOTG) of approximately 200 personnel to the United Arab Emirates in preparation for operations to assist and advise Iraqi Security Forces following an offensive by Islamic State forces. The soldiers were expected to be deployed to Iraq when a legal framework covering their presence in the country was agreed between the Australian and Iraqi Governments. It began moving into Iraq in early November and was tasked with training the Iraq government's Counter Terrorism Service. Personnel from SOTG have also been involved in co-ordinating airstrikes remotely to assist Iraqi forces engaged in clearance operations. From September 2015, the strength of SOTG rotations were reduced to approximately 80 personnel

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