In the scene, Cowles is sitting beside a character named Hanjour, holding a leather briefcase on his lap. The tension in the air is palpable as Cowles has a suppressed 9mm Springfield XD pistol ready at hand, indicating the seriousness of the situation. It is quite clear that Cowles has been instructed by Harvath to respond decisively if Hanjour attempts to make any threatening moves.
The warning given by Harvath adds to the high-stakes atmosphere, as Cowles is prepared to use lethal force if necessary, targeting vital areas to ensure Hanjour understands the gravity of his actions. This illustrates both the perilous circumstances and the lengths to which the characters are willing to go for their safety and mission goals.