The Cosmic Computer by H. Beam Piper

Fifty-two years before, they had come to the mesa in the Badlands and dug a pit on top of it, a thousand feet in diameter and more than five hundred deep, and in it they built a duplicate of the headquarters for Third Fleet-Army Force Command. They built a shaft a hundred feet in diameter like a chimney at one side, and they ran a tunnel out through solid rock to the head of a canyon half a mile away. Then they buried the whole thing. Twelve years later, when the War was over, they sealed both entrances and went away and left it.

For a month each winter, cold rains from the east lashed the desert; for the rest of the year, it was swept by windblown sand. Wiregrass sprouted, and thornbush grew; Nature, the master-camoufleur, completed the work of hiding the forgotten headquarters. Little things not unlike rabbits scampered over it, and bigger things, vaguely foxlike, hunted them. Hunted men came, too, their aircars skimming low. None of them had the least idea what was underneath.