The source of this story is a commercial pilot who flies for a regional airline. This is a secondhand story, in that the source was told the story by others. The source appears to be highly reliable, but the reliability of the initial story is unknown. However, it was related as firsthand knowledge to the source by more than one individual.
The source, as mentioned, is a commercial pilot with a strong interest in Area 51. While socializing with his fellow pilots the topic of Area 51 came up, and he discovered that several of his friends and acquaintances had previously worked for EG&G and Key Air. They had flown the "commuter runs" between Las Vegas and the Groom Lake and the Tonopah Test Range facilities.
That in itself was of some interest, but occasionally they flew to somewhere else in the Nellis Complex. This "somewhere else" is what made the story of such interest to pilots as it was far from routine flying.
Before these flights left Las Vegas, the pilots had to get clearance from NORAD to ensure there weren't any foreign spy satellites overhead. As they approached their destination, they contacted the ground and set up their landing pattern. What made this difficult from a pilot's viewpoint was that there wasn't a runway in sight, only miles of sagebrush covered desert. Then, as they continued their approach a runway suddenly appeared in the midst of this sea of nothingness.
How was this accomplished? According to the pilots, the runway was painted (and perhaps textured) to match the surrounding desert. As the plane approached, sprinklers within the runway were turned on to wet the surface, thus making it stand out from the adjacent terrain. After landing, the passengers quickly got off, as the planes were not allowed to linger. The pilots related that the substantial complex the passengers then entered was camouflaged to look like a series of hills, or may have actually been built partially into the hills.
There is no information as to just what this facility's function is. When asked if he was told the location of the airstrip, the source took out a Las Vegas aircraft sectional chart and indicated a location at the very northern portion of the Test Site: Dead Horse Flat within Area 19. The source wasn't 100% certain of his recollection on this point, and said it could also be in the Gold Flat area, just north of Area 19. This is in the no-man's-land between NTS and the Tonopah Test Range. In either case, the approximate location would be the very far northern reaches of the NTS.
It was the source's recollection that the aircraft involved were primarily 737s. When asked how long a runway would be required, the source (who was quite familiar with 737 operations) said that based upon density altitudes for the area, typical loadings and normal safety factors, 8,000' would be a reasonable minimum.
So, is there a mystery facility at the far northern end of the Test Site? Perhaps, but there may be a difficulty with this story. While an airstrip as described could be hidden quite well visibly, it would be much harder to hide it from satellites carrying multi-spectral scanners. Scanners such as these, with the ability to "look" at things in a number of different wavelengths, can usually see through most camouflage. The good ol' USGS sells just such a thing with their very nice Landsat Thematic Mapper images of the Pahute Mesa and Cactus Flat 1:100,000 maps. No such facility is present on either image, although the old airstrip on Buckboard Mesa shows clearly. There is always the possibility the images have been manipulated in the interest of national security, but we have no such control over the Russians.
The story itself awaits some type of confirmation, but it might be one to keep an eye on.