The reconnaissance group shifted position several times as it gathered information for Admiral William Halsey, Jr.'s United States Third Fleet, but for the submarines on patrol, it proved to be only a month of fighting heavy seas while not encountering any Japanese ships.

Her crew, fortunately at battle stations already, drained the conning tower, surfaced, and recovered the men washed overboard within half an hour.

While shifting to the west on 27 December 1944, Baya sighted a Japanese task force consisting of two heavy cruisers and four destroyers attempting to retreat from the Philippines.

After refit alongside the submarine tender USS Anthedon (AS-24), Baya put to sea once again on 19 February 1945 for her third war patrol, this time in company with the submarine USS Hammerhead (SS-364), and proceeded to a patrol area in the South China Sea off Cap Varella on the coast of Japanese-occupied French Indochina.

The submarines sighted no significant targets until 4 March 1945, when the five-ship Japanese convoy HI-98, consisting of the tanker Palembang Maru, a cargo ship, and three escorts, appeared on Baya′s radar scope.

Numerous sailboats hampered Baya as she attempted to approach the targets, and a calm, moonlit sea gave the advantage to her adversaries.

Two others hit the cargo ship, but Baya could not determine the extent of damage she caused because the escorts drove her deep with depth charges.

Two hours before the start of the midwatch on 20 March 1945, she contacted a single Japanese ship, the auxiliary netlayer Kainan Maru, leaving Phan Rang Bay.

Later that morning, Baya fired another stern tube salvo at a convoy of two escort destroyers and a submarine chaser leaving Phan Rang Bay, but her luck did not hold.

Ordered to the newly liberated Subic Bay on Luzon in the Philippines, Baya arrived there on 27 March 1945 for repairs and a refit alongside the submarine tender USS Howard W. Gilmore (AS-16).

On 29 April 1945, a United States Army Air Forces B-24 Liberator bomber which mistook her for a Japanese submarine dropped a bomb which exploded about 1,500 yards (1,370 m) ahead of Baya while Baya was operating approximately 15 nautical miles (28 km; 17 mi) east-northeast of Pulo Cecil de Mer, French Indochina, at 10°34′N 109°09′E / 10.567°N 109.150°E / 10.567; 109.150.

On 29 and 30 June 1945, Baya and the submarine USS Capitaine (SS-336) conducted a coordinated gun attack on five Japanese small craft.

After an unsuccessful gun attack on another Japanese patrol craft, Baya received orders to proceed to Subic Bay on 26 July 1945.

Two weeks after Japan's capitulation, Baya departed Subic Bay bound for San Francisco, California, which she reached on 24 September 1945, passing under the Golden Gate Bridge as part of Admiral Halsey's symbolic end-of-war parade.

Reclassified as an auxiliary research submarine, AGSS-318, on 12 August 1949, Baya conducted experiments for NEL San Diego, California.

She participated in local operations near San Diego and served with a joint American-Canadian task force gathering scientific data off western Canada in November and December 1948.

In December 1955 she commenced an overhaul at the Hunters Point Naval Shipyard in San Francisco to update her capabilities for NEL testing.

[1][6] Baya served in the Vietnam War zone for two months in 1966 in conjunction with sonar research operations for NEL and in submerged visibility studies for the Naval Oceanographic Office.