From 2004, the strike group has made multiple Middle East deployments providing air forces over Afghanistan and Iraq, as well as conducting Maritime Security Operations.

The strike group received the Humanitarian Service Medal in recognition of its disaster relief efforts in Indonesia during Operation Unified Assistance in 2004–05.

On 20 August 1998, the group took part in Operation Infinite Reach, launching Tomahawk cruise missiles against the Sudanese Al-Shifa pharmaceutical factory.

Also, the group executed 1518 rotary-wing sorties for a total of 4401 flight hours, including flying 1737 humanitarian relief missions in support of Operation Unified Assistance (pictured) between 26 December 2004 and 3 February 2005 following the 2004 Indian Ocean earthquake and tsunami.

[30][31] Also, on 15 April 2006, squadron HSL-47 helicopters and the guided-missile destroyer Russell provided aid to a fishing vessel in distress while operating in the South China Sea.

[33][34] Also, on 9 May, while operating with Combined Task Force 150, the guided-missile destroyer Shoup assisted a disabled dhow by towing it from the Gulf of Aden to Mukalla, Yemen.

[35] The strike group's Composite Unit Training Exercise included Mobile Security Squadron 2 (MSRON-2), Helicopter Visit, Board, Search and Seizure (HVBSS) Team 1, a first for West Coast-based U.S. Navy ships.

[39][40] While en route, the strike group executed carrier qualifications and anti-piracy training, as well as anti-submarine warfare exercises off Guam with the attack submarine Hawaii.

Since 20 October 2010, Carrier Air Wing Two has launched more than 1,800 combat sorties in excess of 10,000 flight hours with a 100 percent completion rate for Afghanistan related missions.

[50] Aircraft from Carrier Strike Group Nine also participated in joint aerial combat training exercises with the Royal Malaysian Air Force on 14 February 2011.

[51] On 22 February 2011, the strike group flagship Abraham Lincoln hosted a Brunei military delegation led by Deputy Minister of Defense Dato Paduka Mustappa Sirat.

[53] On 5 December 2010, the Halsey and the French frigate Tourville participated in a bi-lateral naval gunnery exercise in the Arabian Sea to enhance coalition maritime forces training and coordination.

[54] On 18 January 2011, a sailor from the guided-missile destroyer Halsey was reported overboard in the Gulf of Oman, initiating a search-and-rescue mission involving helicopters from the Halsey, the fast combat support ship USNS Rainier, and the British guided-missile frigate Cumberland, as well as land-based P-3 maritime patrol aircraft and FA-18 strike fighters from Carrier Air Wing Two based on the carrier Abraham Lincoln.

On 19 January, the body of the missing sailor was recovered 75 miles (120.7 km) east of Fujairah, United Arab Emirates, and was identified as Petty Officer Dominique Cruz, 26, of Panama City, Florida.

[55] On 31 January 2011, the cruiser Cape St. George responded to a distress call from a sinking Iranian dhow by dispatching a rescue team via a rigid-hulled inflatable boat (RHIB) (pictured).

[56] On 2 February 2011, the destroyer Momsen, with the cruiser Bunker Hill, responded to a distress call from the Panamanian-flag merchant vessel Duqm in the Gulf of Oman.

[58][59][66] Carrier Strike Group Nine conducted military exercises with France, Bahrain, Malaysia, Singapore, Saudi Arabia, and Oman.

[86] In addition to combat air support for coalition forces in Afghanistan, Carrier Strike Group Nine maintained flights operations some 30 nautical miles (56 km; 35 mi) off the coast of Iran.

[88] On 17 January 2012, the guided-missile destroyer Momsen conducted a boarding party with Explosive Ordnance Disposal Mobile Unit 1131 based on the aircraft carrier Abraham Lincoln.

[89] On 31 January 2012, at 12:37pm local time, an MH-60S Seahawk helicopter from HSC-12 spotted a disabled Iranian fishing dhow, the M/V Sohaila, with nine crew members aboard (pictured).

[91][92] Warships that participated in Stakenet 2012 included the U.S. guided-missile destroyers Sterrett and John Paul Jones and the coastal patrol vessels Typhoon and Chinook; the British frigate Argyll; and the Kuwaiti fast-attack craft Al Nokhetna and Maskan.

[95] On 14 May 2012, during its 2012 deployment, HSM-77 Detachment Five completed its temporary operational rotation on board the British replenishment oiler Fort Victoria which was serving as the flagship for Combined Task Force 151.

[101] On 5 July 2012, the guided-missile destroyer Sterrett returned to Naval Base San Diego, California, completing a seven-month-long deployment to the U.S. Fifth Fleet as a unit of Carrier Strike Group Nine.

[102] On 7 August 2012, the aircraft carrier Abraham Lincoln arrived at its new homebase of Naval Station Norfolk, Virginia, to start its upcoming four-year-long, mid-life overhaul at the Newport News Shipbuilding shipyard.

[100] On 9 December 2010, the U.S. Navy announced that Abraham Lincoln will undergo its scheduled four-year Refueling and Complex Overhaul at the Newport News Shipbuilding shipyard in Virginia.

On 10 January 2012, Ronald Reagan sailed into Puget Sound Naval Shipyard for its 12-month, US$218 million docking planned incremental availability (DPIA) overhaul.

Such FST-J exercises simulate virtual at-sea training involving real-world battle scenarios while the ships of the strike group remained docked in port.

[121] On 18 November 2013, Carrier Strike Group Nine completed its independent deployer certification exercise (IDCERTEX) held in the U.S. Third Fleet area of operations.

The first phase involved such unit-level training as shipboard firefighting; man overboard drills; visit, board, search, and seizure (VBSS); and other ship-specific functions.

[21] On 17 April 2015, Ronald Reagan departed Naval Air Station North Island, California, for sea trials following the completion of its seven-month Planned Incremental Availability (PIA) refit and upkeep cycle.