Following her Refueling and Complex Overhaul in 2001, her home port was changed to Naval Air Station North Island in San Diego County, California.

On 26 May 1981, a Marine Corps EA-6B Prowler assigned to Carrier Air Wing 8 (CVW-8) crashed on the flight deck, killing 14 crewmen and injuring 45 others.

[8] The Prowler was fuel-critical after a "bolter" (missed approach), and its crash and the subsequent fire and explosions destroyed or damaged nineteen other aircraft.

[11] Despite having no connection to the accident, the media focused on the autopsy results of several members of the Nimitz's enlisted flight deck crew who were killed, who tested positive for marijuana.

The ship, in company with USS Forrestal, conducted a Freedom of Navigation exercise in international waters in the Gulf of Sidra near Libya on 18 and 19 August 1981.

After a brief stop in San Diego, to offload the East Coast air wing, Nimitz arrived at her new home port of Bremerton, Washington, on 2 July 1987.

Between 14 and 24 July 1997, Nimitz participated in Joint Task Force Exercise 97-2 (JTFEX 97–2) off the coast of southern California, which also served as a "Revolution in Strike Warfare" demonstration.

The latter event was designed to demonstrate the capability of an aircraft carrier and an embarked air wing to project carrier-based airpower into littoral warfare.

When flight operations were completed four days later, Nimitz and Carrier Air Wing Nine had carried out 771 strike sorties while dropping 1,337 bombs on target.

S-3 Vikings conducted recovery tanking and supplied more than one-third of the fuel passed to Carrier Air Wing Nine aircraft during this surge operation.

[15][16] A following study by the Center for Naval Analyses determined that Nimitz and Carrier Air Wing Nine could have maintained this high-sortie operational tempo for another twelve to twenty-four hours before requiring equipment maintenance, rest for the crews while ordnance and aviation fuel stocks to be replenished.

On 21 September 2001,[18] after sea trials in the Virginia Capes, Nimitz began to transit around South America to the new home port of NAS North Island in San Diego, California, arriving there on 13 November 2001.

From January to May 2002, a four-month post-shakedown maintenance availability was completed at North Island; during this time Advanced Combat Direction System was installed.

Princeton subsequently contacted two Navy F/A-18F fighters from Nimitz whose cockpit instrumentation recorded data and imagery that some pilots interpreted as an object accelerating and maneuvering at extraordinary speeds.

[25] The carrier departed North Island for her thirteenth deployment on 2 April 2007, to the Arabian Sea, relieving USS Dwight D. Eisenhower in support of OIF.

[27] Sailors participated in community work in Chennai prior to departing, on 5 July 2007, along with the destroyer USS Pinckney towards the Persian Gulf, and then returned to North Island on 30 September 2007.

The Nimitz Strike Group, including CVW-11, departed the States for a scheduled Western Pacific deployment on 31 July 2009,[32] and began to fly combat missions in support of Operation Enduring Freedom 21 September.

[33] In January 2010, while in the Persian Gulf, the ship was awarded the Meritorious Unit Commendation for back-to-back deployments in support of the wars in Iraq and Afghanistan in 2007 and 2008.

[39] In March 2012, Nimitz arrived at the new home port of Naval Station Everett in Washington state after more than a year of maintenance work in Bremerton, replacing sister carrier, Abraham Lincoln.

This operation was part of an evaluation of the feasibility of the MV-22 as a potential replacement for the C-2 Greyhound carrier onboard delivery (COD) cargo transport aircraft.

[41][42] The BBC reported that Nimitz was located in the Persian Gulf, ready to contribute to an operation against Syria when President Obama ordered a military strike.

[43][44] It was reported that Nimitz, after eight months at sea, transited the Suez Canal on 20 October 2013, into the U.S. 6th Fleet area of responsibility, where the Navy intended to keep her for a few weeks conducting joint training with allied nations before returning home.

[48] Following the conclusion of the exercise, on 3 November the first F-35C Lightning II to land on an aircraft carrier recovered aboard Nimitz to begin a two-week Development Testing I deployment.

This saw a pair of aircraft from VX-23 undertaking carrier operations of launch, recovery and handling aboard ship in both day and night conditions.

On 31 December, acting Secretary of Defense Chris Miller ordered Nimitz to return directly to her home port following a nearly ten-month deployment in the Fifth Fleet area of operation.

[60] On 3 January 2021, in an abrupt reversal, acting Defense Secretary Miller ordered Nimitz to redeploy due to "Recent threats issued by Iranian leaders against President Trump and other U.S. government officials.

[68] The PBS series Carrier followed the May–November 2005 deployment of Nimitz to the Persian Gulf, documenting the life and shipboard routines of the crew over ten episodes.