In 1988, another medical evacuation to the South African National Antarctic Expedition (SANAE) Station at Vesleskarvet nunatak broke the record for time and distance in a single Antarctic flight.
Another highlight of the 1988 season was the recovery of an LC-130 Hercules that had been buried in ice and snow since its crash in 1971 near Dumont d'Urville Station.
That aircraft was fully restored and operated with VXE-6 until its disestablishment in 1999.

In 1990, VXE-6 moved almost 8,000 passengers and over 6 million pounds of cargo which included five resupply flights to Vostok Station.
That year, VXE-6 also accomplished the first wheeled landing of an LC-130 Hercules on a blue ice surface near Beardmore Glacier.
On 25 October 1991, the first all-female crew took an LC-130 Hercules to "open up" Amundsen-Scott South Pole Station.

1993 saw VXE-6 break many records, including the transportation of nearly 9.4 million pounds of cargo and fuel.
On 3 February 1996, during the squadron's 40th annual deployment to Antarctica, the squadron conducted its last helicopter mission in Antarctica.
The helicopter component of VXE-6 was formally disestablished in April 1996.

1997 marked the beginning of a three-year program designed to transition United States Department of Defense long-range logistic support for the Antarctic Program from the U.S. Navy to the U.S. Air Force, specifically the New York Air National Guard (NYANG).
1998 was marked by the delivery of materials necessary to begin the construction of the new South Pole Station, completed in 2005.

Beginning in 1997, responsibility for long-range logistical support of Operation Deep Freeze was transferred from the VXE-6 squadron to the 109th Airlift Wing of the New York Air National Guard (NYANG).
The transition was planned over a three-year period to avoid any negative impact on operations and to ensure a complete transfer of knowledge from the U.S. Navy unit to the NYANG.
During the 1996/1997 season, VXE-6 operated six aircraft and was augmented by aircraft of the NYANG.
VXE-6 operated five aircraft during the 1997/1998 season, and the number of flight hours was divided roughly equally between VXE-6 and the NYANG.

The United States Air Force, via the 109th Airlift Wing of the Air National Guard, officially took over responsibility as the primary Department of Defense partner for the National Science Foundation in support of the U.S. Antarctic Program at the beginning of the 1998/1999 season.
A new organization, Detachment 13, was formed to manage the overall support from the Department of Defense.
The detachment replaced the NSFA organization.
The main organizations under Detachment 13 were the 109th Airlift Wing of the NYANG, the Navy’s VXE-6 squadron, and Aviation Technical Services.
For the 1998/1999 season, the six LC-130s of the NYANG were augmented by only three LC-130 aircraft of the VXE-6 squadron.

Operation Deep Freeze 1999 was VXE-6's last deployment season in support of the United States Antarctic Program.
On 24 February 1999, following the closure of Amundsen-Scott South Pole Station's summer operations, the last three LC-130R Hercules from VXE-6 returned to Naval Air Station Point Mugu, California.
The squadron was disestablished on 1 April 1999.
Over the course of its existence, VXE-6 logged more than 200,000 flight hours in direct support of United States interests (primarily scientific research) in the Antarctic.
The squadron transported more than 195,000 passengers, delivered over 240 million pounds of dry cargo and nearly 10 million gallons of fuel to numerous sites throughout Antarctica.
In 1988, another medical evacuation to the South African National Antarctic Expedition (SANAE) Station at Vesleskarvet nunatak broke the record for time and distance in a single Antarctic flight. Another highlight of the 1988 season was the recovery of an LC-130 Hercules that had been buried in ice and snow since its crash in 1971 near Dumont d'Urville Station. That aircraft was fully restored and operated with VXE-6 until its disestablishment in 1999.
In 1990, VXE-6 moved almost 8,000 passengers and over 6 million pounds of cargo which included five resupply flights to Vostok Station. That year, VXE-6 also accomplished the first wheeled landing of an LC-130 Hercules on a blue ice surface near Beardmore Glacier. On 25 October 1991, the first all-female crew took an LC-130 Hercules to "open up" Amundsen-Scott South Pole Station.
1993 saw VXE-6 break many records, including the transportation of nearly 9.4 million pounds of cargo and fuel. On 3 February 1996, during the squadron's 40th annual deployment to Antarctica, the squadron conducted its last helicopter mission in Antarctica. The helicopter component of VXE-6 was formally disestablished in April 1996.
1997 marked the beginning of a three-year program designed to transition United States Department of Defense long-range logistic support for the Antarctic Program from the U.S. Navy to the U.S. Air Force, specifically the New York Air National Guard (NYANG). 1998 was marked by the delivery of materials necessary to begin the construction of the new South Pole Station, completed in 2005.
Beginning in 1997, responsibility for long-range logistical support of Operation Deep Freeze was transferred from the VXE-6 squadron to the 109th Airlift Wing of the New York Air National Guard (NYANG). The transition was planned over a three-year period to avoid any negative impact on operations and to ensure a complete transfer of knowledge from the U.S. Navy unit to the NYANG. During the 1996/1997 season, VXE-6 operated six aircraft and was augmented by aircraft of the NYANG. VXE-6 operated five aircraft during the 1997/1998 season, and the number of flight hours was divided roughly equally between VXE-6 and the NYANG.
The United States Air Force, via the 109th Airlift Wing of the Air National Guard, officially took over responsibility as the primary Department of Defense partner for the National Science Foundation in support of the U.S. Antarctic Program at the beginning of the 1998/1999 season. A new organization, Detachment 13, was formed to manage the overall support from the Department of Defense. The detachment replaced the NSFA organization. The main organizations under Detachment 13 were the 109th Airlift Wing of the NYANG, the Navy’s VXE-6 squadron, and Aviation Technical Services. For the 1998/1999 season, the six LC-130s of the NYANG were augmented by only three LC-130 aircraft of the VXE-6 squadron.
Operation Deep Freeze 1999 was VXE-6's last deployment season in support of the United States Antarctic Program. On 24 February 1999, following the closure of Amundsen-Scott South Pole Station's summer operations, the last three LC-130R Hercules from VXE-6 returned to Naval Air Station Point Mugu, California. The squadron was disestablished on 1 April 1999. Over the course of its existence, VXE-6 logged more than 200,000 flight hours in direct support of United States interests (primarily scientific research) in the Antarctic. The squadron transported more than 195,000 passengers, delivered over 240 million pounds of dry cargo and nearly 10 million gallons of fuel to numerous sites throughout Antarctica.
VXE-6