It is explained a few times at this point in the film, in Preston’s meetings with Jurgen (Preston saying so) and with Dupont (Dupont saying so), that Father has never granted an audience with anyone, as the risk of assassination is too great.
But Preston gives an offer that cannot be refused: he will turn in all the leaders of the Resistance in exchange for a meeting with Father.
However, he finds that he must pass the same Challenge that Jurgen administered: another polygraph test. The first question he is posed is “more of a riddle”, as the examiner says: “What would you say is the easiest way to get a weapon away from a Grammaton Cleric?”
He is shocked to find Brandt answering the question for him: “You ask him for it.” He smiles and winks to Preston with a taunt. “I told you, I’d make my career with you, Cleric.”
“Brandt’s job was simple,” Father (Sean Pertwee, son of Dr. Who‘s Jon Pertwee) explains from a telescreen, “to make you feel like you’d won.” He explains it was his idea all along to infiltrate the Resistance with a Cleric who could feel, but didn’t know it yet.
“But, we’ve never met,” claims Preston. Then the second rude awakening comes: the image of Father switches to Vice-Council Dupont, who reveals that the original Father had died and he had assumed his place.