Intersect Bases refer to top secret establishments where the CIA and NSA house the Intersect computer system. There have been several buildings in the series which fit this definition - the location Bryce broke into in "Chuck Versus the Intersect" which housed the original Intersect, the base seen in "Chuck Versus the First Date", which housed the Second Intersect before it exploded, and the base seen in "Chuck Versus the Ring" which housed Intersect 2.0.