In Dec. 1943, Secretary of the Navy Frank Knox visited the newly commissioned Naval Air Reserve Base at Olathe, KS. The following January he ordered VR-3 to be moved there to continue their operation. This resulted in the inauguration of scheduled round trip flights to the west coast Naval installations. VR-3 was the first military unit to operate "Air Evacuation" flights with their aircraft, flying wounded WWII and ill servicemen from Washington to Burbank, CA. It was followed in December with once a week scheduled flights to Toronto Canada with a flag stop in Ottawa Canada. That same month, they inaugurated four daily flights between the east and west coasts. At that time (1944) VR-3 was the first naval unit to have a WAVE (female sailor) assigned, when a Link trainer was obtained.
In 1946 the squadron was relocated to NAS Patuxent River MD. and in 1948 was the original Naval Air Transport Squadron to be transferred to the newly formed Military Air Transport Service (MATS); the combined air transport force of the USAAF and USN. At the time, the unit was flying the Douglas R5D Skymaster (C-54).
In Dec. 1948, the squadron was transferred to the west coast at NAS Moffett Field CA. During their west coast duty, the squadron transitioned to the Douglas R6D Liftmaster (C-118) aircraft and suffered its first fatal accident when a squadron aircraft impacted the Pali Kea peak in the Hawaiian Islands. It was just 15 miles northwest of its scheduled destination. The squadron remained at Moffett until 1957 when it was relocated to McGuire AFB NJ, still operating within MATS under the command of the Naval Air Transport Wing Atlantic.
In Jun. 1963, the squadron retired their Liftmasters for the newly acquired C-130E Hercules medium haul transport. It continued its operation from McGuire until July 1967 when it was disestablished, becoming the last Navy squadron in the combined services Air Mobility Command (AMC). This ended the inter-service partnership that had begun in 1948 and lasted just short of 20 years.
It was only fitting that the oldest active Naval Air Transport Squadron to participate in this highly successful joint command was the last to be deactivated.