Permit embarked members of Admiral Thomas C. Hart's staff at Mariveles Bay on 28 December and evacuated them to the Netherlands' Submarine Base, Surabaya, Java, arriving on 6 February 1942.

She rendezvoused off Corregidor on the night of 15–16 March, took on board 40 officers and enlisted men (including 36 precious cryptanalysts from the intelligence station, CAST),[11] and landed her ammunition.

She headed for repairs at her new base, Fremantle, Western Australia, after minor damage suffered eluding three enemy destroyers on 18 March.

Permit departed Fremantle on 5 May, and until 11 June was engaged in her fifth war patrol off Makassar, Celebes Island and in the enemy shipping route stretching towards Balikpapan, Borneo.

She made her sixth war patrol en route to Pearl Harbor - from 12 July-30 August - and shortly departed for the United States, entering Mare Island Navy Yard on 9 September for overhaul.

Just after midnight, she spotted a two-ship convoy headed for the Korean coast, and with a salvo of two torpedoes sank Showa Maru in five minutes.

On 28 May 1944 a PV-1 Ventura patrol bomber of U.S. Navy Bombing Squadron 148 (VB-148) mistakenly attacked her in the Pacific Ocean in the vicinity of 06°45′N 151°52′E / 6.750°N 151.867°E / 6.750; 151.867, damaging her with a depth charge .

On 21 September, she departed to relieve Tarpon on lifeguard duty off Truk, and on 11 November ended her 14th and last war patrol at Pearl Harbor.

In mid-May, she sailed to the Submarine Base, New London, Connecticut, to serve as a schoolship until 30 October, when she entered Boston Naval Shipyard for inactivation.

Her name was stricken from the Naval Vessel Register on 26 July 1956; her hulk was sold for scrap to A.G. Schoonmaker, Inc., New York City on 28 June 1958.