When Theodore Bagwell was looking through Gretchen's file, he mentioned her apparently-deceased father. She worked for the Company as an operative, and conceived her child - Emily Morgan - from Jonathan Krantz who was presumably her lover at the time. Gretchen shows, through early flashbacks, how she was imprisoned and tortured during the Iraq war, something but also empathetic in her weaker moments. When she is tortured by General Zavala, Zavala observes how she does not break down during torture, and notes that it is not the first time she has been tortured.
She appeared hiding her scratch on her cheeks with make up. Later, she lured Lincoln to meet her at Garfield Price Building by telling L.J. Burrows, whom she hold as hostage, to inform Lincoln