After transiting Balabac Strait on 22 September, Bonefish continued on to her patrol area in the central part of the South China Sea.

Minesweeper W.12 picked up the Japanese survivors although recently released documents state that W.12 machine-gunned the surviving POWs (a minimum of 250) in the water,[7] On 1 December, the boat sighted a convoy of three ships with two escorts hugging the Celebes coast.

In two separate attacks, the submarine scored a hit on a large passenger/cargo ship Nichiryo Maru which later sank and another on a destroyer escort which apparently survived.

On 11 December, she surfaced to engage small cargo vessel Toyohime Maru [7] with gunfire, scoring several hits before a mechanical problem put her gun out of action.

The next day, the boat made a submerged approach on an unidentified Japanese vessel and fired six torpedoes, scoring one hit; Bonefish never learned the fate of her target.

As she maneuvered into attack position, Bonefish selected a large oiler as her primary target and launched four bow "fish" at it.

Bonefish managed to evade the escorts, and her crew heard explosions which they interpreted as at least two hits on the oiler and one on the cargo ship.

[8] The submarine escaped damage from both the destroyer's depth charges and from aerial bombs which enemy aircraft dropped, but they prevented her from observing the results of her attack.

The submarine maneuvered into a position suitable to attack Tokiwa Maru, launched four torpedoes, and then turned to evade the escorts.

The next day, Bonefish fired a spread of four torpedoes at a cargo ship headed for Davao Gulf but, in spite of three hits, failed to sink the target.

While in the Sulu Sea on 3 May, Bonefish approached a convoy but was forced to dive when an enemy plane dropped two depth bombs which exploded close aboard.

On 14 May, Bonefish approached a convoy of three tankers and three escorting destroyers, steaming off Tawitawi in the Philippines and headed for Sibutu Passage.

Postwar records show that, while her torpedoes only damaged the tanker, they sank one of the escorting destroyers, Inazuma, which was known for having rescued 376 survivors from HMS Exeter and 151 from USS Pope during the Second Battle of the Java Sea.

On 29 July, Bonefish commenced tracking a large, but empty, tanker with escorts and, early the next morning, gained a favorable attack position.

The target, Kokuyo Maru, immediately settled by the stern, and Bonefish headed for the traffic lanes north of Sibutu and Tawitawi.

Bonefish tracked the target whose rapidly falling speed indicated her distress until the crippled tanker's escorts forced the boat to retire.

Patrolling in the vicinity of Cape Bolinao on 10 October, the boats attacked a convoy of cargo ships, and Bonefish scored three hits for undetermined damage.

She departed her lifeguard station the next day, stopped at Saipan for fuel on the 27th, and continued on to Pearl Harbor, where she arrived on 8 November.

From Hawaii, Bonefish continued on to San Francisco, California, where she underwent overhaul at the Bethlehem Steel Submarine Repair Basin from 18 November 1944 to 13 February 1945.

While on lifeguard duty off Korea's southern coast on 16 April, Bonefish rescued two Japanese aviators who had been shot down by a Navy plane.

Equipped with a new mine-detecting device, the submarines were ordered to penetrate the Sea of Japan to sever the last of the Japanese overseas supply lines.

Bonefish successfully threaded her way through the minefields by Tsushima Island as she transited the Korea Strait to enter the Sea of Japan for an offensive patrol off the west central coast of Honshū.