Most aircraft that are no longer needed in frontline service are flown to , the 309th Aerospace Maintenance and Regeneration Group. That’s AMARG, but it was AMARC for so long that it is still mainly known by that name. The yard is attached to Davis-Monthan Air Force Base near Tucson, Arizona. You can drive much of the fence-line and I recall decades ago looking at the forest of B-52 tails and the sad, tailless 707s (vertical stabilizers taken for the aged KC-135s). I also saw about 50 F-86s stacked like cord wood at the back fence. It was sad.
DM has nice runways, so getting there is not an issue. For the most part, the Air Force will van Naval Aviators to the commercial field in Tucson and they fly on an airliner back to their bases. I’m not sure how the Air Force guys get back, but assume it’s similar. Unless you’re hauling a lot of people or cargo, military transport can be uneconomical.
I was slated to stick with my A-6 squadron for that last summer, flying up the rest of the hours and taking the birds down to the desert. Unfortunately, they pushed my orders forward and I had to spend the summer in the central valley in California, reeking of cotton and cow poop. My cruise roommates got the idyllic summer days in the Pacific Northwest, running jets into the Tucson Sun. If they requested, they could take a quick tour, which was cool. I got the VIP tour back in college (my best friend’s dad was the Ops Chief) and it was fascinating.