He had started the Unmarked program, in order to serve The Dark Lord without raising any suspicion. Once he got word that Proudfoot was given carte blanche to use the Imperius Curse to hunt down and kill known Death Eaters, Percy quickly set about flipping the Auror's loyalties by absconding him and putting him under multiple layers of a Confundus, sealing them in his mind so that the magic that ensured his loyalty to the Ministry were fooled as he instead served The Dark Lord's wishes and would have ordinary citizens hunting down the Undesirables.