Clarey was executive officer on board
Dolphin at
Pearl Harbor when the
Japanese attacked the Naval Base on December 7, 1941, and subsequently made one war patrol in
Dolphin to the
Marshall Islands. After commissioning the
Amberjack (SS-219) at
New London,
Connecticut, on June 19, 1942, he completed two war patrols in
Amberjack off
Bougainville and
Guadalcanal Islands as executive officer. During the first war patrol, which lasted fifty-seven days, the Amberjack sank the 19,000-ton Japanese ship
Tonan Maru, a 5,000-ton transport and a 7,000-ton cargo ship. She also delivered 9,000 gallons of aviation fuel, 200 100-pound bombs and a number of
US Army Air Corps pilots to
Tulagi. On her second war patrol, lasting fifty-one days, she scored one direct hit on a 4,000-ton freighter while patrolling south of
Shortland, near
Treasury Island. "For conspicuous gallantry and intrepidity in action in the performance of his duties in the USS Amberjack during a war patrol of that vessel..." he was awarded the
Silver Star. The citation further states: "As Assistant Approach Officer, his outstanding skill, excellent judgement and thorough knowledge of attack problems assisted his Commanding Officer considerably in conducting a series of successful torpedo attacks, which resulted in the sinking and damaging of enemy ships totalling more than 43,000-tons. In addition, he was of great assistance in conducting a successful reconnaissance of four enemy positions and completing a vital special mission, contributing immensely to the success of his vessel in evading extremely severe enemy countermeasures..." Clarey made one additional patrol to the
South Pacific as a prospective commanding officer (PCO) in the submarine
Peto (SS-265). On January 1, 1944, he became the
commanding officer of the new submarine
Pintado (SS-387) at
Portsmouth, New Hampshire. Under his command,
Pintado reached the Pacific in May 1944, and on her first war patrol in the area west of the
Marianas and south of
Formosa on a dark night in June, surfaced and fired six bow torpedoes at a Japanese convoy, making direct hits on two targets with all six torpedoes. Later between the
Marianas and
Luzon she sank three freighters and damaged a large freighter. Clarey was awarded the
Navy Cross with the following citation: For extraordinary heroism as Commanding Officer of the USS Pintado, during the first war patrol of that vessel in enemy Japanese-controlled waters, from May 16 to July 1, 1944. Maneuvering his ship through powerful escort screens, Lieutenant Commander Clarey launched repeated aggressive attacks to sink three Japanese freighters and damage a large freighter despite severe hostile countermeasures... He was awarded a second Navy Cross, denoted by a
Gold Star affixed to the suspension and
service ribbon of his original medal, "For extraordinary heroism during
Pintados second war patrol in enemy-infested waters from July 24, 1944 to September 14, 1944". The citation states: "He pressed home a series of aggressive torpedo attacks against heavily escorted enemy ships, sinking two freighters and a large whaling ship of nearly 20,000-tons and maneuvered successfully and avoided damage to his submarine". He was awarded a third Navy Cross, denoted by a second Gold Star affixed to the suspension and service ribbon of his original medal, for
Pintados third war patrol, in enemy-controlled waters of the South China Sea, between October 9, 1944, and January 1, 1945. The citation states: "Carrying out his duties as Officer in Tactical Command, Commander Clarey skillfully directed the coordinated search for his attack group known as "Clarey's Crushers", against a retiring enemy Task Force and contributed to the destruction of a Japanese light cruiser. He further led his submarines in an attack to sink a destroyer and damage an aircraft carrier. On the night of December 12–13, he conducted three surface attacks, in heavy seas, to sink two enemy merchantmen, which contributed to Pintado's sinking of over 40,000-tons of Japanese shipping". Clarey also wore a ribbon for the
Presidential Unit Citation awarded to
Pintado. Detached from
Pintado in April 1945, he was assigned to the staff of
Commander Submarine Force Pacific Fleet (COMSUBPAC) and was serving in that assignment at the cessation of hostilities in August 1945. ==Post-war, through late 1950s==