Not much is known about Cowan's early history except that before the show he had been ordered by his superiors to burn Michael Westen and Victor Stecker-Epps. He also became one of Management's operatives but that seemed to be against his will.
Eventually Michael and Cowan met up, and Michael confronted him about burning him. Cowan told him that the reason behind his burn notice was bigger than either of them and that the people he worked for had plans for him. Before he could give Michael any critical information, however, he was shot by an assassin working for Carla.