The carrier's fifth deployment commenced in August 2000 when Abraham Lincoln again traveled to the Persian Gulf in support of Southern Watch. On this deployment, the carrier, air wing and battle group ships earned the Navy Meritorious Unit Commendation. Additionally the ship earned the prestigious Arleigh Burke Award as the most improved command in the Pacific Fleet.
Abraham Lincoln was in port on 11 September 2001. She was put to sea on 20 July 2002 to support Operation Enduring Freedom. She took up station once more in support of Operation Southern Watch before taking a port visit to Perth, Western Australia. It was during this time that the Lincoln was ordered to the Persian Gulf to take part in Operation Iraqi Freedom. This forced the Navy to extend Lincoln's stay from 20 January 2003 to 6 May 2003. The news of this extension was delivered to the ship's crew on New Year's morning by the then Battlegroup Commander, RADM Kelly, with the phrase, "We don't need to be home holding our loved ones, we need to be here holding the line. Get over it!" The term "Get over it" became the running joke aboard ship, which eventually led to a deployment patch made aboard that read "Westpac 2003 CVN-72 CVW-14 GET OVER IT" with an image intended to depict an admiral kicking a sailor in the groin.
Abraham Lincoln and the carrier battle group and airwing helped deliver the opening salvos and air strikes in Operation Iraqi Freedom. During her deployment, some 16,500 sorties were flown and 1.6 million pounds of ordnance used. Sea Control Squadron 35 (VS-35), the "Blue Wolves", was instrumental in delivering over 1 million pounds of fuel to these strike aircraft, one of the largest aerial refueling undertakings by a carrier aviation squadron in history. The carrier returned home in May 2003, in the process receiving a visit from President George W. Bush before officially ending Lincoln's deployment by docking at San Diego before returning to homeport in Everett, WA. Bush stated at the time that this was the end to major combat operations in Iraq. While this statement did coincide with an end to the conventional phase of the war, Bush's assertion—and the sign itself—became controversial after guerrilla warfare in Iraq increased during the Iraqi insurgency. The vast majority of casualties, both military and civilian, have occurred since the speech. The White House said their services constructed the banner. As explained by Cmdr. Conrad Chun, a Navy spokesman, "The banner was a Navy idea, the ship's idea. The idea popped up in one of the meetings aboard the ship preparing for its homecoming and thought it would be good to have a banner, 'Mission Accomplished.' The sailors then asked if the White House could get the sign made. ... The banner signified the successful completion of the ship's deployment," Cmdr. Chun continued noting that the Abraham Lincoln was deployed 290 days, longer than any other nuclear-powered aircraft carrier in history.
On 1 October 2004, the carrier's controlling formation was redesignated from Cruiser-Destroyer Group Three to Carrier Strike Group Nine. Abraham Lincoln departed for her next voyage on 15 October 2004. The carrier was on a port call in Hong Kong when the 9.0-magnitude 2004 Indian Ocean earthquake struck southern Asia on 26 December 2004. To help with the international relief effort and assist with search and rescue efforts already underway, the Lincoln deployed to the hard hit western coast of Sumatra to provide humanitarian assistance. The deployment was designated Operation Unified Assistance. Abraham Lincoln's Air Transportation Office (ATO) coordinated the flow of supplies into the region, and the carrier provided air traffic control for the relief effort. Sailors from the Abraham Lincoln's Engineering Department Repair Division designed a potable water manifold to help bring fresh water to Aceh Province, Sumatra, with the system beginning to ship the much-needed fresh water on 4 January. In total, Carrier Strike Group Three delivered 5,929,000,000 pounds (2.689×109 kg) of relief and Humanitarian supplies, including 2,915,500 pounds (1,322,400 kg) of food and 748,410 pounds (339,470 kg) of medical supplies, during Operation Unified Assistance (OUA). Carrier Strike Group received the Humanitarian Service Medal in recognition of its humanitarian assistance/disaster response (HA/DR) efforts during the OUA mission.
In mid-January 2005 the carrier left Indonesian waters after the Indonesian government refused to allow fighter pilots assigned to Lincoln to conduct air patrols and training flights. By law, US carrier-based pilots must practice at least once every two to three weeks to remain "fit," otherwise they are grounded. Despite the move into international waters, Lincoln continued to provide support to the region until 4 February. During the carrier's 33 days on station, she and her battle group, Carrier Strike Group Nine delivered 5.7 million pounds of relief supplies. The 17 helicopters assigned to HSL-47 Saberhawks and HS-2 "Golden Falcons", attached to CVW-2 flew 1,747 relief missions along the western coast of Sumatra. The carrier's departure coincided with the arrival of the hospital ship Mercy.
Between 7 March – 27 May 2005, Abraham Lincoln underwent a docking planned incremental availability (DPIA) yard overhaul at Naval Station Everett, Washington, and following its subsequent sustainment training, the carrier underwent an additional planned incremental availability (PIA) at NS Everett between 28 June – 26 August 2005. Between 1–23 June 2005, Abraham Lincoln and Carrier Air Wing Two (CVW-2) trained in the northern Pacific, conducting their quarterly Integrated Strike Group (ISG) Sustainment Training cycle. Abraham Lincoln carried out surge sustainment training for the Fleet Response Plan (FRP), fleet replacement squadron carrier qualifications (CQ), and Joint Task Force Exercise 2005 (JTFEX-05) in southern Californian waters between 19 October and 16 November 2005. For JTFEX-05, Abraham Lincoln and Carrier Air Wing Two were joined by the guided-missile cruiser Mobile Bay; the guided-missile destroyers Russell and Shoup, and Carrier Strike Group Seven led by the nuclear-powered aircraft carrier USS Ronald Reagan (CVN-76).
On 18 December 2006, the Abraham Lincoln left dry dock at the shipyard ahead of schedule and under budget. The Puget Sound Naval Shipyard and Intermediate Maintenance Facility (PSNS & IMF) completed ship tank maintenance in less than half the scheduled time. In 89 days, 18 tanks were completed. The Tank Value Stream Team achieved this partnering with Ship’s Force and the Lincoln Project Team. While in dry dock, the whole ship was painted by the crew at nights and on weekends rather than waiting for contractors to do the job.
On 5 January 2006, the carrier Abraham Lincoln departed its homeport of Everett, Washington, and transited to San Diego, California, for its scheduled underway period to undertake its sustainment training exercisies (SUSTAINEX) and post-refit inspection by the U.S. Navy's Board of Inspection and Survey (INSURV). Lincoln completed its additional sustainment training in southern Californian waters between 21–24 February 2006.
The refit was completed 26 March 2007, when Rear Adm. Scott Van Buskirk assumed command of Carrier Strike Group Nine (CSG 9) from Rear Adm. Bill Goodwin.
On 29 August 2006, the carrier Abraham Lincoln arrived at Naval Base Kitsap in Bremerton, Washington, and on 8 September 2006, the carrier entered Dry Dock No. 6 at the Puget Sound Naval Shipyard & Intermediate Maintenance Facility (PSNS & IMF) to begin a scheduled Docked Planned Incremental Availability (DPIA) yard maintenance period. Major projects for this DPIA included the refurbishment of ship tanks, work on three of the four catapults, modernization of navigation systems, resurfacing of the flight deck, and updates to the ship’s Local Area Network (LAN). Lincoln also received installation of the RIM-116 Rolling Airframe Missile (RAM) system, which improved the ship’s close range defensive capabilities. On 18 December 2008, Lincoln left dry dock ahead of schedule and under budget because PSNS & IMF yard team was able to cut the time of ship tank maintenance by more than half, completing 18 tanks in 89 days.
The aircraft carrier Abraham Lincoln held a fast cruise from the pier between 23–25 June and left Puget Sound on 26 June to conduct sea trials before returning to its homeport of Naval Station Everett, Washington, on 30 June 2007.
Abraham Lincoln underwent flight deck carrier (FDC) Qualifications while sailing in southern Californian waters between 12–15 July 2007. F/A-18E Super Hornets and F/A-18C Hornets from strike squadrons VFA-137 and VFA-151 joined VX-23 test pilots performed precision approach drills to ensure that the ship’s equipment, such as the Precision Approach Landing System (PALS), operated within close tolerances, with SH-60B Seahawks from squadron HS-2 providing search and rescue (SAR) capabilities during flight operations.
On 20 August 2007, Abraham Lincoln and embarked Carrier Air Wing Two completed their 25-day Tailored Ship’s Training Availability (TSTA) and Final Evaluation Problem (FEP) training period off southern California. TSTA is designed to prepare the ship and crew for full integration into a carrier strike group, and FEP is a graded 48-hour evolution to evaluate how well the units learned during TSTA. Lincoln and embarked CVW-2 aircraft conducted over 1,000 fixed-wing sorties. Lincoln completed five replenishments at sea (RAS) evolutions, including two with the fleet replenishment oiler Henry J. Kaiser, and participated in 18 general quarters (GQ) drills. Also, on 13 August, Lincoln tested its defensive capabilities when she fired four RIM-7P NATO Sea Sparrow missiles, with two of them at BQM-74E Chukar remote-operated aerial target drones.
Carrier Strike Group Nine's Composite Unit Training Exercise (COMPTUEX) featured twenty-four Sailors from Mobile Security Squadron 2 (MSRON-2), Helicopter Visit, Board, Search and Seizure (HVBSS) Team 1 (pictured), a first for West Coast-based U.S. Navy ships. MSRON-2 Team 1 specializes in boarding non-compliant ships at sea in the dead of night, detaining the crew if necessary, and identifying suspected terrorists or subjects of interest, using the element of surprise afforded by helicopter insertion, night vision equipment, and state-of-the-art biometrics. MSRON-2 HVBSS Team 1 was established in 2004 at Norfolk Naval Shipyard in Portsmouth, Virginia, and it was the first team of its kind to reach operational status.
Also, on 11 November 2007, n HH-60H Seahawk helicopter from squadron HS-2 crashed while operating from the ship approximately 100 miles (160 km) from San Diego. Rescuers successfully pulled all seven crewmembers from the water.
Between 3–30 January 2008, Carrier Strike Group Nine (CARSTRKGRU 9) conducted antisubmarine exercises (USWEx) and Joint Task Force Exercise 03-08 (JTFEx 03-08) off southern California. On 16 January, Secretary of the Navy Donald C. Winter visited the strike group's flagship, the Abraham Lincoln. On 20 January, a NATO Boeing E-3A Sentry Airborne Warning and Control System (AWACS) aircraft was deployed from NATO Air Base Geilenkirchen, Germany, with a multi-national crew aboard for JTFEx 03-08, and it defended Carrier Strike Group Nine from a simulated air attack (30 January).
The Abraham Lincoln began its planned incremental availability (PIA) maintenance cycle at the Puget Sound Naval Shipyard (PSNS) in Bremerton, Washington, on 16 April 2008. The objective of this PIA yard period is to refurbish the Lincoln's shipboard system to meet the anticipated 50-year service life of the ship, including an upgraded Local Area Network system. Beginning 1 December 2009, Lincoln began daily flying squad, general quarters (GQ), and integrated training team (ITT) drills in preparation for its first underway period following its current maintenance cycle.