It's 1885 and Maggie Gilkeson (CATE BLANCHETT) is trying to raise her two daughters, Lilly (EVAN RACHEL WOOD) and Dot (JENNA BOYD), on her New Mexico farm where her hired help, Brake Baldwin (AARON ECKHART) and another man, work.
Out of the blue, her long-estranged father, Jones (TOMMY LEE JONES), shows up one day hoping for reconciliation. Maggie wants no part of that, however, as she's never forgiven him for abandoning her when she was just a child. Thus, she sends him on his way and hopes the matter is behind her.
When several men are murdered and Lilly is kidnapped, however, Maggie is forced to ask Jones, who sees himself as an Indian, to help find her. With the army forces, led by Lt. Jim Ducharme (VAL KILMER), appearing incompetent and headed in the wrong direction, Jones agrees to lead Maggie and Dot in the rescue attempt.
Their task is daunting, however, since the renegade kidnappers are larger in number and are led by Pesh-Chidin (ERIC SCHWEIG), a former Apache scout for the army who's turned bad and supposedly wields supernatural powers. Eventually enlisting the aid of Indian acquaintance Kayitah (JAY TAVARE) and his adult son, Honesco (SIMON BAKER), Jones and Maggie hope to find and rescue Lilly before Pesh-Chidin and his men get to Mexico where they plan on selling Lilly and other kidnapped girls.