Black Rock is a secret subterranean Fulcrum base, seen in "Chuck Versus the Colonel", located beneath the disused Starbrite drive-in theatre. The GPS coordinates given for the base are 34 53' 56.40", -117 1' 19.20" (34.899000, -117.022000 which in reality is the center of downtown Barstow, CA).
It was here Fulcrum kept Stephen Bartowski imprisoned whilst he worked on building Fulcrum their own Intersect, known as the Fulcrum Intersect, after the first base of operations, the Strength Leader Corporation was infiltrated by Team Bartowski and had to be abandoned. This base looked to the outside world as simply an abandoned drive-in so much so that it fooled even Sarah and Chuck at the start of the episode.
This base was infiltrated by Team Bartowski after Stephen left Chuck a clueas to his presence there. The arrival of Team Bartowski coincided with the arrival of dozens of Fulcrum operatives who were intended to become an army of human Intersects, and the Starbrite was to be the location of the mass upload, making them all the best operatives in the world.
Stephen, however, had programmed the Intersect cube to overwrite the existing Intersect files in his son's brain, removing the Intersect and freeing Chuck, rather than create any more human Intersects. The base was then destroyed by an air raid ordered by General Beckman.
It is unknown if any Fulcrum agents survived the air raid, other than Ted Roark who was seen after the raid intent on reaching the Bartowkis and the Intersect Cube.