Wonderfully textured and layered, "The Truth Will Out" was by far my favorite episode. Every character is in a place he/she feels uncomfortable--Will in his apartment and office due to the bugs, Tanya due to her drug problems, Miles due to taking the file, Grant due to his daughter's play, and Katherine due to people looking around in her house.
With the usage of the FBI taking over API to track a leak, the writers deftly distill the innermost feelings of the employees and lays them out for us to see. The polygraph tests we see aren't used to find the leak--the perpetrator a random guy led off near the end--but force the characters into situations where they are completely tied down, trapped in a room with a machine which can force out the truth.
And we also see the mind-numbing, bureaucratic nature of government work, the strict adherence to rules which prevents Grant from making a single call or forces Spangler to take the polygraph.
The mystery side of the Rubicon still hasn't picked up, and it's getting to the point where I don't care about it either way. I'd be perfectly content to watch the goings-on at API without the cloak-and-dagger spy stuff hovering in the background. But it's also a structural problem, in part, because Will and Katherine are isolated in their hunt and the enormity of their positions have yet to come out.
Score: 9.3/10