Keating returned to the Naval Military Personnel Command in September 1995 as Director, Aviation Officer Distribution Division (Pers 43). He then served as the Deputy Director for Operations (Current Operations/J33), with the Operations Directorate of the Joint Staff (JS J-3) in Washington, D.C., from August 1996 until June 1998. He assumed command of Carrier Group Five, home ported in Yokosuka, Japan, in June 1998, embarking aboard both and . In September 2000, Admiral Keating reported to OPNAV in Washington as Deputy Chief of Naval Operations for Plans, Policy and Operations (N3/N5). In February 2002, he assumed command of United States Naval Forces Central Command and United States Fifth Fleet in Manama, Bahrain. From October 13, 2003 to October 21, 2004, Keating served as the Director, Joint Staff. Keating commanded of United States Northern Command and the North American Aerospace Defense Command from 5 November 2004 to 23 March 2007. Keating became Commander, United States Pacific Command on 26 March 2007. He served as ComPac until 19 October 2009, just before his retirement.