Looks to me like Kerry (as SOS) is the target (going by State Dept. notable). Rudy on Howie Carr (Jackass Comey) is starting a pissing contest betwen Comey and Brennan, but I think those two can bring down Kerry.
Howie Carr speaks to the average Joe in MA / NE. Rudy calling Comey a jackass isn't unusual , rather, fits in with the dialog Howie uses.
I'm going with Comey being the weakest link and Rudy (Tagteaming with Trey G) with is offering him an out. Comey (I think), Mueller and Durham operated in Boston at some point. Mueller a classmate of Kerry in HS. Howie's been on Kerry's ass for years and Howie was all over the Bulger stuff as well.
Rudy is the one you don't fuck with in this movie, and Howie can help get the message out to the area as they prepare the take down. Nobody better than Howie for this in Boston. After that the show moves to NYC.