General Beckman stands in the room containing the Second Intersect
The Second Intersect (beta intersect), is a computer system which started being constructed right after "Pilot" and finished in Chuck Versus the First Date.
The new system was nearing completion by the end of 2007; however in "Chuck Versus the First Date", development may have been delayed by the theft of the Cipher by Fulcrum. The Cipher is described as "the brains of the Intersect, the most important piece."
The module was installed and the system activated by Director Graham, who had brought in several of his agents to receive the subliminal imprinting. Fulcrum sabotaged this by replacing the Cipher with a decoy which led to the destruction of the Beta Intersect, killing Graham and the agents with him.