Doctrine in the inter-war years emphasized the submarine as a scout for the battle fleet, and also extreme caution in command. Both these axioms were proven wrong after the attack on Pearl Harbor in December 1941. The submarine skippers of the fleet boats of World War II waged a very effective campaign against Japanese merchant vessels, eventually repeating and surpassing Germany's initial success during the Battle of the Atlantic against the United Kingdom.^[2]

During the war, submarines of the United States Navy were responsible for 55% of Japan's merchant marine losses; other Allied navies added to the toll.^[4] The war against shipping was the single most decisive factor in the collapse of the Japanese economy.^[2]

The Navy adopted an official policy of unrestricted submarine warfare, and it appears the policy was executed without the knowledge or prior consent of the government.^[5] The London Naval Treaty, to which the U.S. was signatory,^[5] required submarines to abide by prize rules (commonly known as "cruiser rules"). It did not prohibit arming merchantmen,^[5] but arming them, or having them report contact with submarines (or raiders), made them de facto naval auxiliaries and removed the protection of the cruiser rules.^[6][7] This made restrictions on submarines effectively moot.^[5] U.S. Navy submarines also conducted reconnaissance patrols, landed special forces and guerrilla troops and performed search and rescue tasks.^[8]

In addition to sinking Japanese merchant ships, postwar records compiled by the Joint Army-Navy Assessment Committee indicate Japan lost 686 warships of 500 gross tons (GRT) or larger to submarines during 1,600 war patrols. Only 1.6 percent of the total U.S. naval manpower was responsible for America's success on its Pacific high seas; more than half of the total tonnage sunk was credited to U.S. submarines. The tremendous accomplishments of American submarines were achieved at the expense of 52 subs with 374 officers and 3,131 enlisted volunteers lost during combat against Japan; Japan lost 128 submarines during the Second World War in Pacific waters. American casualty counts represent 16 percent of the U.S. operational submarine officer corps and 13 percent of its enlisted force.

In addition to their commerce raiding role, submarines also proved valuable in air-sea rescue.^[9] While in command of United States Navy aircraft carrier task force 50.1 Rear Admiral Charles Alan Pownall, proposed to Admiral Charles A. Lockwood (commander of Pacific Fleet Submarine Force) that submarines be stationed near targeted islands during aerial attacks.^[10] In what became known as the "Lifeboat League", pilots were informed that they could ditch their damaged planes near these submarines (or bail out nearby) and be rescued by them. Eventually the rescue of downed American pilots became the second most important submarine mission after the destruction of Japanese shipping.^[11] Initially, the rescue submarines met several obstacles, most important of which was the lack of communication between the submarines and aircraft in the area; this led to several Lifeguard League submarines being bombed or strafed, possibly including the sinking of USS Seawolf (SS-197) and USS Dorado (SS-248) by American planes.^[10]

As fighting in the Pacific theater intensified and broadened in geographic scope, the eventual creation of Standing Operating Procedure (SOP TWO) led to several improvements such as the assignment of nearby submarines before air attacks, and the institution of reference points to allow pilots to report their location in the clear.^[11] After the capture of the Marianas, targets such as Tokyo, about 1,500 mi (2,400 km) north of the Marianas, were brought within range of B-29 attacks and Lifeguard League submarines began rescue operations along their flight paths.^[11] Submarine lifeguards spent a combined 3,272 days on rescue duty and rescued 502 men.^[11] Famous examples include the rescue of 22 airmen by the USS Tang,^[12] and the rescue of future U.S. President George H. W. Bush by the USS Finback (SS-230)