Clarke was hospitalized for exhaustion and a heart condition in 1943. After returning from medical leave, he served from January to October 1944 as Chief of Staff to the Commander Amphibious Training Command, Atlantic Fleet, which trained crews for the landings in Sicily, Anzio, Normandy, and southern France. The Secretary of the Navy, James Forrestal, signed a citation awarding Capt. Clarke a Gold Star in lieu of a second Legion of Merit for his work in this "assignment of vital importance...the establishment and maintenance of a high state of combat readiness of amphibious ships and craft."