The submarine departed Hawaii on 9 October 1942, headed via Midway Island for "Imperial Waters" (the seas surrounding The Empire of Japan), and conducted training dives and battle surface drills en route.

However, after sighting several outbound freighters about 1 nautical mile (1.9 km) from the coast, executive officer Frederick "Fritz" Harlfinger II (who later commanded Trigger) convinced Azer that the mines be planted as close in as possible.

After an unsuccessful search for a disabled sampan, Whale made rendezvous with an escort and proceeded to Pearl Harbor where she underwent repairs from 10 November 1942 through 2 January 1943.

After conducting training dives and drills en route, she arrived in the Wotje and Kwajalein area on 10 January for two days' patrol off those atolls.

Within six minutes, 3,559 ton Iwashiro Maru had sunk about 40 nautical miles north of Kwajalein, 09°54'N, 167°07'E., and Whale resumed her voyage toward Truk, running submerged.

On 25 January while on a surface patrol along the Truk–Empire line, Whale sighted smoke in the bright moonlight and fired a three-torpedo spread from the stern tubes at the target.

A fourth torpedo also failed to explode, and the target, transport Shoan Maru (5624 GRT) attacked in the central Pacific in position 14°24'N, 153°30'E.turned away from the submarine, presenting only her stern to view.

"The thought of the fuel expended," her commanding officer lamented, "on the long, endaround runs, coupled with the loss of the torpedoes themselves, made 'heartbreaking' but an inadequate euphemism."

She refueled there, had her last torpedo removed, and sailed for Hawaii the following day, conducting daily training of gun crews and test dives for radio reception en route.

Whale fired another three-torpedo spread at the second freighter and soon heard two heavy explosions followed by a deep, rumbling detonation with the accompanying water noises which suggested that a ship was breaking up.

The continual pounding in heavy seas had cracked a number of battery jars, bringing the total of disabled cells to 10 forward and 13 aft.

After one torpedo hit, 7,148 ton Naruto Maru stopped dead in her tracks, listed to starboard and started going down slowly by the stern.

Whale fired another torpedo which hit amidships and prodded the ship into sinking faster; the vessel sank northwest of the Mariana Islands in position 24°12'N, 142°52'E.

On 24 August, Whale positioned herself 20 nautical miles (37 km) west of Kusakaki Shima and intercepted an enemy convoy headed for Nagasaki.

Whale launched three torpedoes and sank the larger of the freighters, transport ship Denmark Maru (5869 GRT) about 400 nautical miles southeast of Okinawa in position 23°09'N, 135°14'E.

The target seemed undamaged except for a slight trim down by the bow, and it was imperative that the ship be sunk expeditiously in order to avoid further depth charges by the escorts.

Whale fired another stern shot which hit squarely under the stack, and the target, Tarushima Maru,(4865 GRT, torpedoed earlier that day by USS Seawolf) in position 22°50'N, 135°40'E.

On 24 January, she made contact with an enemy submarine and attempted an end-around, but her maneuver was thwarted by a fire in the trim pump which filled the control room with smoke, forcing Whale to surface.

A casualty to the starboard propeller necessitated a trip to Pearl Harbor, and it was not until 13 March that Whale returned to Midway, the staging port for her seventh patrol.

The next day, Whale got underway for a rendezvous point where she joined submarine Pollack (SS-180) on 23 March and patrolled along a likely shipping route east of Tori Shima and the Bonins.

Immediately, depth charges began to drop, Whale cleared the area to the southeast and later received a report of a crippled freighter in tow 120 nautical miles (220 km) north of her.

Whale arrived at Tanapag Harbor, Saipan, on 3 September and the next day got underway in company with the other "Bears" and coastal minesweeper Heed (AMC-100) which acted as their escort.

She spent the next eight days making emergency repairs and conducting training dives, patrolling on station, and submerging to avoid detection by unidentified aircraft.

On 29 September, she made rendezvous with Seahorse, received written instructions for conducting the remainder of the patrol; and set her course for a new station southwest of Formosa.

The submarine arrived on station on 3 October and submerged some 60 miles (97 km) north of Cape Borjeador, Luzon, and patrolled around Calayan and Dalupiri islands in the Babuyan group.

Whale was harassed by plane contacts throughout the daylight hours of 16 October and she ordered to take a new station at the southwest end of Ryukyu Shoto in anticipation of a Japanese fleet sortie which never occurred.

On 4 and 5 January 1945, Whale and sister ship Kingfish (SS-234) searched unsuccessfully in the waters near Sufu Gan for a life raft containing 11 survivors of a downed B-29 Superfortress.

As a result of this lifeguard duty, Whale discovered many flaws in the air-sea rescue doctrine and made several noteworthy recommendations to improve future operations.

Whale commenced patrol east of Okino Shima on 30 July and ran into heavy seas: "Couldn't hold our own with this current, so took soundings each half hour."

On 9 August, Whale received 16 aviators and one patient who were transferred from submarine Blackfish (SS-221), using a rubber boat with lines on bow and stern for propulsion.