During the 2003 U.S. invasion of Iraq, Rogers joined the military's Joint Staff, which works for the Joint Chiefs of Staff, where he specialized in computer network attacks. From 2007 onward he served as director of intelligence for the military's Pacific Command. In 2009, he became director of intelligence for the Joint Chiefs of Staff, and was subsequently named commander of U.S. Fleet Cyber Command and commander of the U.S. 10th Fleet, with responsibility for all of the Navy's cyberwarfare efforts. As such, Rogers was the first restricted line officer to serve as a numbered fleet commander and the first Information Warfare Community (IWC) officer to achieve the rank of vice admiral.