For the next three years he served in the armored cruiser Frederick, including convoy escort duty in the North Atlantic during World War I.

[2] For six months after the Pacific War began in December 1941, Wilkes, who was soon promoted to Captain, commanded Asiatic Fleet submarines during their frustrating struggle against the fast-moving tide of Japanese conquest.

[2] On 29 December 1941 Wilkes and his headquarters staff were forced to evacuate from Corregidor Island in the submarine Swordfish, and headed for Surabaya, Java.

[3] Following his return to the United States in mid-1942, Wilkes attended the Naval War College, then became Commanding Officer of the new light cruiser Birmingham, taking her to the Mediterranean Sea to participate in the invasion of Sicily in July 1943.

[2] A few months after World War II ended, he returned to the U.S. to command the Atlantic Fleet's submarine force, a position he held from late December 1945 until March 1947.

He then had duty with the Joint Chiefs of Staff, in Washington, D.C., before going to Europe to take command of Naval Forces, Germany, in August 1948.