Following Coronado, Miller was assigned as the Operations Officer for the Seventh Fleet on board USS Blue Ridge (LCC-19), home ported in Yokosuka, Japan.

He returned to John F. Kennedy in August 1999 as her 23rd Commanding Officer, and left almost immediately for an extended deployment to the Persian Gulf.

Miller was commissioned as a Deputy Assistant to the President and the first-ever active duty Director of the White House Military Office in November 2002.

[2] On 3 August 2010, Miller relieved Vice Admiral Jeffrey Fowler as Superintendent of the United States Naval Academy.

[4] In February 2015, Miller received a Letter of Censure from Secretary of the Navy Ray Mabus involving Glenn Marine Defense Asia (GDMA), during his tour as Carrier Strike Group Commander while on board the USS Ronald Reagan.