[1] In 1919 and 1920, Lieutenant Commander Cooke repeated the process for the larger submarine USS S-5 (SS-110), distinguishing himself when she accidentally sank on 1 September 1920 by saving the lives of 37 men trapped in her wreck.

[1] During the remainder of the 1920s, he was executive officer of the submarine tender USS Rainbow (AS-7), had shore duty at the Cavite and Mare Island Navy Yards, was gunnery officer of the battleship USS Idaho (BB-42), and served at the United States Department of the Navy in Washington, D.C. From 1931 to 1933, Commander Cooke commanded a submarine division, attended the Naval War College Senior Course, was Commandant of the Guantanamo Bay Naval Base, had further Navy Department duty and was war plans and logistics officer with the United States Fleet staff.

[1] Promoted to captain in June 1938, Cooke soon returned to Washington, D.C., for duty with the Chief of Naval Operations' war plans staff.

He took command of the battleship USS Pennsylvania (BB-38) in February 1941, saw her through the 7 December 1941 Japanese attack on Pearl Harbor, Hawaii, that brought the United States into World War II, and remained with her into 1942.

He played a vital role on King's staff as a brilliant strategist[2] until after the end of World War II in 1945, serving as Chief of Naval Plans and as Advocate for Naval Management of War in Pacific and working on issues related to the Navy's transition from a battleship-centered orientation to one focused on aircraft carrier task forces.