After searching Chichagof Harbor and the waters off Kiska Island, the submarine engaged in an indecisive gunnery duel with a freighter on 23 August.
Heading for the Japan-Kwajalein shipping lanes, she tracked a freighter the morning of 20 February and closed to sink troop transport Shinkoku Maru (3,991 tons) that night.
While northeast of Truk on 3 March, she detected the naval auxiliary Nichiyu Maru (6,818 tons) and attacked, but was driven off by the fire of deck guns.
Halibut detected, tracked, and attacked a convoy bound for Truk from Kisarazu, Japan, putting a single torpedo (out of a spread of six) into the side of IJN troop transport Aikoku Maru (10,437 tons).
Together with Searaven and Pompano, she cruised towards her assigned patrol zone off the east coasts of Honshū and Hokkaido, including the Tsugaru Strait.
The following day the sub headed into Iburi Wan; she sighted one convoy but was unable to close, but later sank the 6,581-ton freighter Taibun Maru, with three bow shots.
Two small patrol boats saw the sinking and dropped 24 depth charges after Halibut, which escaped by unintentionally passing through a minefield.
That night Halibut made radar contact with a vessel identified as a destroyer but later found to be the light cruiser Nachi, firing the submarine's remaining aft torpedoes in a rough sea for no hits.
Halibut stopped briefly at Midway for fuel and food before sailing to a full refit at Pearl Harbor, arriving on 16 September.
[9] A short time later, while performing underwater training, Halibut was accidentally struck by a destroyer; the glancing blow damaged both periscopes (an incident which in peacetime would warrant a board of inquiry).
Halibut sailed from Pearl Harbor on her seventh war patrol on 10 October 1943, headed for the approaches to the Bungo Suido.
She reached Midway after four days travel and stopped briefly to top up her fuel tanks (having consumed 14,000 gallons already) and to repair a defective motor-generator for her new SJ radar.
She reached Okinoshima on 25 October and quickly found her daylight activities constrained by a heavy fishing sampan presence.
Halibut was detected and the escort drove her off and held her at bay with fifteen depth charge attacks as the freighter fled.
She went on to patrol the approaches to Van Diemen Strait just south of Kagoshima, before returning north when she received an Ultra message indicating a Japanese task force, including an aircraft carrier, near the Bungo Suido.
Halibut dove to more than 350 feet (110 m) to avoid attacks from three destroyer escorts; in the event, only thirteen depth charges were dropped.
On her eighth war patrol (beginning at Pearl Harbor on 14 December) Halibut formed a coordinated attack group, or "wolf pack", with Haddock and Tullibee.
The very first USN wolf pack had left Midway on 1 October 1943 – Cero, Shad, and Grayback claimed five ships sunk and eight damaged (post-war analysis indicated only three sinkings).
Operating independently, Halibut patrolled Port Apra and Tanapag Harbor on her way home, observing a Katori-class cruiser near Saipan, and being attacked by aircraft and depth charges on 23 January while attempting a stealthy approach on the Taiyō-class escort carrier Unyō in Garapan Anchorage[10] (the carrier had already been damaged by Haddock).
The submarine was then forced into evasive action as a bomber arrived overhead; the aircraft and two patrol boats dropped some ninety depth charges without ever endangering Halibut.
On 1 May she spotted a compact group of eighteen 250-ton sampans while east of Okinawa and trailed them southwards; after dusk she surfaced and closed the range to attack with her deck armaments from 1,000 yards (910 m).
She rendezvoused with Perch after six days travel, and a fully qualified doctor from Midway aboard the second sub was transferred to Halibut by boat.
Again it was decided to leave the injured man aboard rather than risk moving him, and the submarine was refueled and restored before heading on to a major overhaul at the ship repair basin of Bethlehem Steel at Sixteenth Street in south San Francisco, California, with ninety days rest for the crew.
On her tenth war patrol Halibut again joined a coordinated attack group, this time with Haddock and Tuna, under the overall command of John P. Roach.
The group departed Pearl on 8 October, bypassing Midway and taking a 3,650-mile (5,870 km) great circle route towards Tanapag, Saipan, which had been captured in June.
The group reached the Luzon Strait on 25 October, but mid-morning the submarines were ordered to set up scouting lines to intercept units of the Japanese fleet retiring after the Battle off Cape Engaño.
Spread out east-west 30 nautical miles (56 km) apart, the submarines moved rapidly until enemy ships (heavily engaged by USN dive bombers) were detected around 17:30.
An hour after the attack, Halibut resurfaced and headed north chasing a radar contact, which she lost in the early morning of 26 October.
As Halibut submerged and turned away, the crew heard a "loud, fast buzzing noise" which was quickly followed by five explosions (apparently jikitanchiki-equipped Mitsubishi G3M aircraft).
The submarine went down to 325 feet (99 m) as she detected the sonar of two escorts when a sudden near explosion severely damaged the conning tower, which had been abandoned.