on 13 October, departed Pearl Harbor for her third war patrol. After touching at Midway Island on 17 October, she headed for the Mariana Islands, where she reconnoitered Pagan Island and Agrihan Island on 25 October and 26 October, and Farallon de Pajoras on 1 November and 2 November. On the last date, she struck an uncharted pinnacle; but suffering no apparent damage, continued her patrol. On 3 November, she was off Maug; and, two days later, she sighted her first target, a Mogami class cruiser. Squalls interfered, however, and she abandoned the target after a four-hour chase. On 7 November, she was back off Agrihan; and, on 8 November, she closed with a freighter, which turned and gave chase. The freighter was a Q-ship, a warship disguised as a merchantman. Unable to regain the advantage, Scorpion retired.
Poor weather continued to plague the submarine's hunting until, on 13 November, she sighted a freighter and a tanker escorted by three warships. Firing her torpedoes, she scored on the oiler, which went dead in the water. One of the escorts dropped depth charges, then rejoined the formation. On 14 November, Scorpion patrolled near Rota; and, on 15 November, she watched for targets off Saipan.
For the next week, the submarine continued to work the shipping lanes of the Mariana Islands without success. Heavy seas and squalls continued to shelter enemy traffic. On 22 November, she sighted a transport accompanied by two destroyers and a corvette. She stalked the formation for 16 hours but was unable to fire. A few hours later, low on fuel, she headed home.