Maria Hill joined S.H.I.E.L.D. and rose to the position of commander. After Colonel Nicholas Fury's "Secret War", Maria was chosen to be director of SHIELD by the President himself. Although many others who she herself admitted were better suited for position were not considered for directorship, she was assigned director. It has emerged that Maria was chosen as the other candidates were "Fury Loyalists" and S.H.I.E.L.D. needed "new direction".
Before the "Superhuman Registration Act" was passed as law, Hill met with Captain America aboard the helicarrier and proposed that he lead the Avengers within the law and arrest anyone who would not comply. Captain America declined her offer, stating that he would not arrest people who risk their lives for their country every day of the week. Upon his failure to comply, Hill ordered her superhuman response team or "cape killers" to tranquilize Captain America. During the scuffle Rogers avoided being tranquilized and escaped becoming the de facto leader of the Secret Avengers.
After the "Civil War" had ended, Hill stepped down as director, giving the position to Tony Stark and resumed her duties as commander for S.H.I.E.L.D.