The USS Nimitz's eleventh operational deployment began on March 3, 2003. It relieved the USS Abraham Lincoln in the Persian Gulf in April 2003, launching Carrier Air Wing 11 aircraft sorties over Iraq in support of Operation Iraqi Freedom (OIF) and Afghanistan in support of Operation Enduring Freedom (OEF).

The USS Nimitz returned to San Diego in November 2003. Nimitz and Carrier Air Wing Eleven (CVW-11) were awarded the 2003 Battle "E" and Flatley Award in early 2004.

In May 2005, Nimitz again with CVW-11 embarked on a deployment to the Persian Gulf. It returned to the U.S. in November 2005. This deployment marked three decades of service, and was depicted in the Emmy award winning 2008 PBS documentary series Carrier. In June 2006, Nimitz was awarded the 2005 Battle "E".

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