Steaming via New Caledonia and the New Hebrides, she arrived at Rendova, British Solomon Islands, on 14 January 1944 to begin duty with Motor Torpedo Boat Squadrons, South Pacific (SOPAC).

During the greater part of August 1944 she operated at Aitape Harbor, tending Motor Torpedo Boat Squadron (MTBRBon) 33 and providing assistance in salvage work.

Arriving there on 31 August 1944, she was engaged in fueling, provisioning and making final repairs to the PT boats of the squadron preparatory to sailing for Morotai as a unit of Task Group 70.1.

[1] Making temporary repairs, she remained at Morotai, tending PT boats of Task Unit 70.1.2 and PBYs now ranging over the Netherlands East Indies on relief and intelligence and reconnaissance missions, until February 1945.

[1] During February and March 1945, Mobjack transported materiel, spares, and advanced base personnel as she accompanied motor torpedo boat squadrons to forward areas.

Arriving on 11 April 1945, she disembarked her passengers and steamed on to Palawan, where she relieved motor torpedo boat tender USS Willoughby (AGP-9) as the repair unit for MTBRons 20 and 23.

For four days Mobjack fueled and sustained the motor torpedo boats assigned to night patrol off the coast to prevent the Japanese from replacing naval mines, restoring obstacles blown by underwater demolition teams, or disturbing channel markers planted by the minesweepers.

[8][9] In August 1955, Pioneer began the west coast survey off southern California at an east–west line spacing of 5 nmi (5.8 mi; 9.3 km) with Mason and the magnetometer aboard.

The resulting magnetic intensity charts showed north–south lineations and a 875 km (472 nmi; 544 mi) lateral offset at the along the Murray fracture zone.

[9] Mason published results of the Murray fracture zone in 1958 in the Geophysical Journal of the Royal Astronomical Society titled "A Magnetic Survey off the West Coast of the United States Between Latitudes 32° and 36° N and Longitudes 121° and 128°".

The stripes indicated both periodic reversals of the earth's magnetic poles and the steady creation of new rocks which spread across the sea bottom as the ocean floor moved, making a record of these changes in polarity.

Mason's work aboard Pioneer with the fluxgate magnetometer thus revealed "magnetic striping" on the floor of the Pacific, the first time it had been noted anywhere and a major discovery in the development of the theory of plate tectonics.

[9][10][11] Pioneer continued offshore hydrographic work in the Pacific Ocean off the U.S. West Coast – at one point holding an open house while in port – until 5 March 1957, when she departed San Francisco for the Territory of Hawaii, where she conducted electronic-position-indicator- (EPI-) guided basic survey operations north of the Hawaiian Islands under direction of the U.S. Navy along with two U.S. Navy survey ships.

[13] Upon completing this, she deployed to the Western Pacific, where she cooperated with the U.S. Navy oceanographic survey ship USS Rehoboth (AGS-50) – also a former Barnegat-class seaplane tender – and the United States Army cable ship USACS Albert J. Myer in completing 65,196 square nautical miles (223,622 square kilometers) of hydrography around Wake Island and Eniwetok Atoll, guided by LORAN, LORAN-C, and EPI.

[14] On 9 September 1959, Pioneer departed California, stopped at Pearl Harbor, Hawaii, and then proceeded to Kwajalein Atoll, where she performed hydrographic survey operations in support of a classified U.S. Navy project.

On 24 March 1960, she departed Alameda bound for Pearl Harbor – running a deep-sea sounding line for the Commander, Pacific Missile Test Range, along the way – and resumed hydrographic operations under SHORAN control.

[16] Prior to the 1961 field season, Pioneer underwent major repairs to her hull plating, and the Coast and Geodetic Survey equipped her with a gravity meter and a towed transducer.

[17] Pioneer then set out from Kodiak to conduct ocean surveys in the North Pacific Ocean between the Aleutian Islands and Hawaiian Islands to the limit of LORAN-C control, during which she again released weather balloons and made frequent meteorological reports, conducted bathymetric measurements, employed her magnetometer and gravity meter, took bottom core samples in Shelikof Strait, discovered a layer of warm water at depths of 320 to 440 feet (98 to 134 meters) between 50 degrees and 53 degrees North latitude, across all sounding lines, and discovered eleven seamounts.

[18][19] Pioneer underwent an overhaul, then conducted trials of a new deep-sea anchoring winch installed aboard her before departing Oakland on 9 August 1962 and returning to her survey of the North Pacific, running a sounding line along 36 degrees 30 minutes North latitude as well as taking gravimetric, meteorological, and magnetic measurements, and she made oceanographic observations in the Aleutian Trench.

After calling at Naval Station Kodiak for supplies, she departed Kodiak on 1 September 1962, ran a magnetic survey and gravimetric transect of about 1,400 nautical miles (2,600 kilometres) for the University of California, and resumed her North Pacific survey, making further gravimetric, magnetic field, bathythermograph, current, and meteorological observations and conducting underwater photography.

She ran gravity transects northeast of Hilo and east of Oahu before departing Hawaii, concluding the 1962 season with deep-sea sounding lines during her return to California, where she arrived at San Francisco on 31 October 1962.

Between 7 and 14 February she ran a deep-sea sounding line into the survey area in the North Pacific, then continued survey work she had left incomplete in 1961, including weather observations, almost continuous use of her gravity meter and magnetometer, and deep-sea sounding lines from Hawaii to San Francisco and return that each crossed the gravity meter test range.

After a port call, she put to sea again on 1 May 1963, making Nansen bottle casts, collecting bottom samples – including a seven-foot (2.1-meter) core sample taken at a depth of 22,170 feet (6,760 meters) in the Aleutian Trench – studying currents with drift bottles and a geomagnetic electrokinematograph, photographing the ocean bottom, and taking bathythermograph measurements.

[24] Leaving Singapore on 27 March 1964, she proceeded through the Strait of Malacca, stopped at Penang Island in Malaysia, then crossed the Andaman Sea, Bay of Bengal, and Indian Ocean – becoming the first ship in the history of the United States Coast Survey or U.S. Coast and Geodetic Survey to visit the Indian Ocean – to the mouth of India's Hooghly River, where a harbor pilot met her and conned her up the river to a berth in Calcutta.

In the South China Sea, she dredged the bottom in the vicinity of Seahorse Shoal and her scuba divers examined the peak of the seamount there for 30 minutes and took color photographs of it.

She ran one line across the gravity meter test range prior to entering San Francisco Bay and surveyed the waters around the piers of the Golden Gate Bridge.

She completed her 1964 cruise with her arrival at San Francisco on 11 August 1964, exactly six months after she departed, having covered 31,507 nautical miles (58,351 km; 36,258 mi) since her departure.

[22] In early 1965, Pioneer ran deep-sea track lines between California and Hawaii, making oceanographic observations, and investigating a reported seamount that rose to 5,850 feet (1,780 meters) below the surface.