Pretty easy, you know near the end of season 4 i think it is they show an FBI lady in a limo calling Bertram and asking to be kept in the loop on the red john case, then the camera moves up to kirkland - wham thats him, everybody is always reporting to him. He's controlling, later in season 5 he is manipulating Bertram to be kept in the loop again, he keeps taking suspects and jumping in when cases are obviously nothing to do with homeland security, he's just using his connections to find out how much the cops know. Also i am pretty certain the aircon guys that break into Janes room are some of his men disguised from homeland security.