On 9 February 2001, while conducting a main ballast tank blow off the coast of Oahu while hosting several civilian "distinguished visitors", mainly donors to the Battleship Missouri Memorial, Greeneville struck the 191-foot (58 m) Japanese fishery high school training ship Ehime Maru (えひめ丸), causing the fishing boat to sink in less than ten minutes with the death of nine crew members, including four high school students.

However, after he faced a court of inquiry, it was decided a full court-martial would be unnecessary and opted for a non-judicial punishment; Commander Waddle's request to retire was approved for 1 October 2001 with an honorable discharge.

The boat's underside, rudder, and propulsion train suffered minor damage; repairs required drydocking and a significant delay in the remainder of her deployment.

"[7] Hankins was selected for promotion to Captain in 2005 and served as Commodore of Submarine Squadron One (COMSUBRON 1) based in Pearl Harbor, Hawaii.

Between 25 and 27 March 2006, a series of anti-submarine warfare exercises were held in Hawaiian waters that included Greeneville; Carrier Strike Group Nine; the nuclear-powered attack submarines Seawolf, Cheyenne, Tucson, and Pasadena, as well as land-based P-3 Orion aircraft from patrol squadrons VP-4, VP-9, and VP-47.

[8][9] In October 2007, Greeneville left her home port of Pearl Harbor to conduct a Depot Modernization Period at Portsmouth Naval Shipyard in Kittery, ME.