Black Rock is a secret Fulcrum base, seen in "Chuck Versus the Colonel", which is located underground, beneath a disused drive-in cinema. The GPS coordinates given for the base are 34 53' 56.40", -117 1' 19.20" (34.899000, -117.022000 which in real life is the center of downtown Barstow, CA). This is where 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 room as simply an abandoned drive-in, which fooled Sarah and Chuck at the start of the episode.
This base was also infiltrated by Team Bartowski in the episode after Stephen left Chuck a clue to his presents in the base. At the time the base was being used by Fulcrum to upload the finished Intersect into hundreds of Fulcrum agents, making them all Human Intersects and therefore the best soldiers and agents in the world. This didn't work however as Stephen had programmed the Intersect to over right the existing Intersect files in his head, removing the Intersect. Before Fulcrum had the chance to force Stephan to reconfigure the Intersect to put its self inside the agents heads the base was destroyed by the air raid that General Beckman ordered. It is unknown how many Fulcrum agents survived the air raid, as we only see Ted Roark afterwards.