Continuing operations in the San Diego area for the next several years, Plunger joined Holland (AS–3) and five Porpoise-class boats 15 March 1938 for a cruise to Dutch Harbor, Alaska.

Plunger, commanded by David Charles White (Class of 1927) set out on her first patrol less than a week after the Pearl Harbor attack, but had to turn back due to a pressure hull leak.

Her orders sent her to Kii Suido, a principal entrance into the Inland Sea and an important funnel to industrial bases in the area.

Through diplomatic channels, President Roosevelt had arranged an exchange of political prisoners trapped in the United States and Japan by the outbreak of war, including U.S.

They were put aboard the neutral vessels Asama Maru and S.S. Conte Verde for transfer from Japan to the United States.

In the early morning hours of 30 June, he picked up Conte Verde and began an approach, somewhat astonished to find a ship all lighted up.

Back at Pearl Harbor, George "Turkey Neck" Crawford was on duty that night in submarine headquarters.

On Plunger, White had Conte Verde fixed in his periscope hairs and the crew at battle stations when his communications officer, having picked up and just decoded this fifth immunity message, rushed up into the conning tower.

On 2 November while patrolling off of Maringe Lagoon, lookouts sighted an airplane and Plunger submerged to avoid detection.

Immediately thereafter Plunger's hull hit midship on the coral reef destroying her sound gear and damaging her bottom.

After repairing at Brisbane, Plunger returned to the Guadalcanal area for her fourth war patrol and operated off Munda, where Japanese barges were coming in at night, unloading troops and supplies, and departing by daybreak.

In June, she joined Lapon (SS-260) and Permit (SS-178) in the first U.S. penetration into the Sea of Japan, an area abounding with Japanese shipping.

Returning to Pearl Harbor 5 September, the ships were the only U.S. vessels to complete two patrols to this area until the final weeks of the war.

She added lifeguard duties to her resume as U.S. bombers hit the islands, picking up a downed aviator 15 November.

Frequent depth charge attacks pursued Plunger in January 1944 as she patrolled off the Japanese main islands.

She departed 15 February 1945 for New London, to serve in a training capacity until 25 October, when she reported to New Haven for Navy Day celebrations.