She departed on 1 May 1941 for the Caribbean Sea, transiting the Panama Canal on 9 May, stopping in San Diego, California, through 21 May, and arriving at Pearl Harbor, Hawaii, on 31 May.

She operated from the Hawaiian Islands into the fall of 1941, as tensions rose in the Far East and the United States prepared for war in both the Pacific and Atlantic Oceans.

Thresher and her sister ship USS Tautog (SS-199) departed Submarine Base Pearl Harbor on 31 October 1941 on a simulated war patrol north of Midway Atoll in the Northwestern Hawaiian Islands.

Escorted by the destroyer USS Litchfield (DD-336) through Hawaiian waters lest she be mistaken for a hostile submarine, Thresher received word at 08:10 that Pearl Harbor was under attack by Japanese aircraft.

Litchfield promptly set off to join American light forces departing from the harbor, leaving Thresher alone to conduct her first real war patrol.

She again tried to enter the harbor on 8 December, but was driven off by depth-bombs from a patrol plane, before Thornton (AVD-11) finally arrived to provide safe conduct for the boat at midday.

Reconnoitering Majuro, Arno, and Mili atolls from 9 to 13 January 1942, she shifted to waters off Japanese-held Guam in the early morning darkness of 4 February.

There, she was to gather weather data off Honshū for use by Admiral William Halsey's task force (the carriers Enterprise (CV-6) and Hornet (CV-8), then approaching Japan.

Embarked in Hornet were 16 United States Army Air Forces B-25 Mitchell medium bombers, under the command of Lieutenant Colonel James H. Doolittle, intended to attack Tokyo on 18 April.

Shaken but not seriously damaged, Thresher made minor repairs as she headed for Truk to reconnoiter the passes leading into this enemy naval bastion.

Since she had been reassigned to the Southwest Pacific Submarine Force, Thresher sailed away from this encounter en route to Australian waters and terminated her fourth war patrol at Fremantle on 15 August.

These strategic mine fields laid by Thresher and her sisters in subsequent patrols, covered Japanese shipping lanes in areas of the Southwest Pacific Command previously unpatrolled by submarines.

Later, these minefields filled the gap between patrol zones along the coastal waters of Malaya, Siam, and Indochina, when many boats were diverted to participate in the Solomon Islands campaign.

While reconnoitering off Balikpapan, Borneo, and the Celebes coast, Thresher sighted a tanker aground on a reef off Kapoposang Island in the Java Sea.

Rising to periscope depth, the boat observed the second ship in the column down by the bow, with her stern up in the air and her screws, still revolving, out of the water.

[11] After arriving back in Fremantle on 10 January 1943, the boat got underway 15 days later for her seventh war patrol, with four torpedoes short of a normal load.

Her eighth war patrol (commanded by Harry Hull, Class of 1932), lasting 4 April to 23 May 1943, was uneventful, but her ninth saw the boat score another kill.

Newly refitted and again commanded by Harry Hull, Thresher departed the west coast on 8 October 1943 and arrived at Pearl Harbor one week later; she commenced her tenth war patrol on 1 November, bound for the waters north of the Caroline Islands.

Prowling north of Truk, Thresher commenced tracking a five-ship convoy on the morning of 12 November and slipped past two escorts shortly before midnight.

After remaining overhead two hours, dropping between ten and fifteen more depth charges,[15] the enemy finally turned away, leaving Thresher unscathed.

On 26 January, Thresher made radar contact with a small convoy and soon spotted two ships steaming along beneath the overcast night skies.

All four main engine overspeed trips were actuated; cork insulation flew; lights broke; clocks stopped; and water poured down the antenna trunk.

On 28 and 29 January, Thresher patrolled the Formosa-to-Palau route, in the Luzon Strait, before returning via Midway Island to Pearl Harbor where she arrived on 18 February.

She remained on air-sea rescue ("lifeguard") station during American carrier strikes on Truk, bombarded Oroluk Atoll on 11 April, and photographed islands in that group.

Commencing a reload of her tubes at midnight (00.00 or 24.00), Thresher returned to the area and continued the attack on the convoy which consisted now of only three ships: a freighter, the oiler, and an escort.

Six days later, while cruising on the surface, Thresher was battered by heavy seas which caused the boat to roll some 53 degrees from the vertical and produced waves up to 50 feet (15 m) high.

Rounding the southern tip of Kyūshū, Thresher sighted several small craft before making contact with a minelayer and two subchasers on 10 September.

By 21:00, Thresher had maneuvered into position off the enemy's port bow and waited for the Japanese ships to make a zig which would place her at a desirable point for the attack.

Attacking from the bright moon side, Thresher fired two bow tubes, aiming one torpedo at the hull near the mainmast and one at the foremast.

The episode, entitled "The Thresher Story," recounts the events of firing her 3" gun on her Fifth war patrol and being subsequently refitted with "an old relic," a 5"/51 (which had entered service in 1911).