In 2006 Malone made her Broadway stage debut as Sister James in a production of the Tony Award-winning play "". Ben Brantley of "The New York Times" wrote that Malone "slides effortlessly and appealingly into the part of the dewy, impressionable Sister James." She also appeared in films, co-starring with Chloë Sevigny in filmmaker M. Blash's improvised feature "Lying" (2006), playing one of several women attending a precarious weekend gathering. Malone followed this with supporting roles in the independent comedy "The Go-Getter" (2007), playing a young woman reunited with her middle school crush, and the biographical drama "Into the Wild" (2007), in which she portrayed the sister of Chris McCandless.