It's not clear to me what the problem from A, B, and C's perspective is: the actual threat is from a group unrelated to B or C, secretly funded by an organization unrelated to A. So, why would their grift get uncovered as a result of stopping the threat? Or maybe I missed something in that description. It's okay for the plot not to make sense, the plots of technothrillers never make sense anyway.
My understanding: In this scenario B and C are low-bid government contractors. C gets a bid from the FBI (that indirectly involves them in the DHS' larger game). B gets caught up because they (are built to) contract C and then do a bunch of analysis of C's data and C is set up for deniability so the (semi-anonymized) data from the FBI's contract/game gets sent to B too. B's alarm bells go off and they raise the flag to A, because that is who contracts them (and what they were built to do). A as a tiny counter-espionage bureau dealing with the alarms B sends them is where the other alarms go off and embroils them directly in DHS' larger game (probably even through some fun chain of command game up to the President and back down). (Then the retasks funnel back down to A from DHS to B to C in such a way to ensure DHS' deniability and lock A, B, and C in DHS' problems [and eventually their doom].)