The first submarine tender to be stationed at Midway was the Fulton from July through October 1942. Midway's submarine base personnel worked in conjunction with the submarine tenders, and they had the capacity to refit up to four submarines at a time. This capacity was similar to the ability of a single submarine tender. In 1944, in addition to the tenders working in the submarine basin/inner harbor, a 2,500-ton floating Auxiliary Repair Dry Dock (ARD) arrived. The ARD provided Midway's Submarine Base almost the same capability to repair/refit submarines as Pearl Harbor's Submarine Base.

The "Silent Service" was partially responsible for the U.S. bringing the war in the Pacific to a quicker close. Despite early nagging problems of defective torpedoes, the Submarine Force destroyed 1,314 enemy ships in the Pacific, representing fifty-five percent of all enemy ships lost and a total of 5.3 million tons of shipping. Out of 16,000 submariners, the force lost 375 officers and 3,131 enlisted men in 52 submarines, and although this was a tragic loss, it was still the lowest casualty rate of any combatant submarine service on either side in the 1939-1945 conflicts. A total of 15 submarines were lost from Midway. These submarines last touched U.S. soil at Sand Island - Midway Atoll. A total of 1,203 submariners were lost from Midway and are on "Eternal Patrol".

In 1950, the Navy decommissioned Naval Air Station Midway, only to re-commission it again to support the Korean conflict. Again, Midway supported Far Eastern operations. Thousands of troops on ships and planes stopped at Midway for refueling and emergency repairs.

During the Cold War, the U.S. established a super-secret underwater listening post at Midway in an attempt to track Soviet submarines. These sensitive devices could pick up whale songs for miles and the facility remained top-secret until its demolition at the end of the Cold War. "Willy Victor" radar planes flew night and day as part of the DEW Line (Distant Early Warning), and antenna fields covered the islands.

With about 3,500 people living on Sand Island, Midway supported the Vietnam effort. The Officer-in-Charge house or "Midway House" was used in June 1969, when President Nixon met "secretly" with Republic of South Vietnam President Thieu.

In 1978, the Navy downgraded Midway from a Naval Air Station to a Naval Air Facility and large numbers of personnel and dependents began leaving the island.

With the conflict in Vietnam over, and the introduction of spy satellites and nuclear submarines, Midway's significance to National security began to diminish.