Capelin put out on her second war patrol on 17 November 1943, in the Molucca and Celebes Seas, and was to pay particular attention to the trade routes in the vicinity of Siaoe, Sangi, Talaud, and Sarangani Islands. She was to end her patrol on 6 December.
USS Bonefish (SS 223) communicated with Capelin on 1 December 1943 in the area assigned to Capelin at that time. Bonefish warned Capelin about a convoy they had just attacked. Capelin acknowledged the message was never heard from again.
Japanese records studied after the war listed an attack by minelayer Wakataka on a supposed United States submarine on 23 November, off Kaoe Bay, Halmahera. The Japanese ship noted the attack produced oily black water columns that contained wood and cork splinters and later a raft was found. This is the only reported attack in the appropriate area at that time. Also, Japanese minefields are now known to have been placed in various positions along the north coast of Sulawesi (Celebes) in Capelin’s area, and she may have been lost because of a mine explosion. Gone without a trace with 76 crew members, Capelin remains in the list of ships lost without a known cause.