She won an Emmy Award for her performance as Clothilde in the 1976 network miniseries "Rich Man, Poor Man". Her weekly-series stints have included Aunt Molly Culhane in "How the West Was Won" (1977), which earned her a second Emmy Award nomination. She did multiple appearances on "Murder, She Wrote", one of them as Freida, a secretary aiding Jessica Fletcher in finding a murderer on the episode "Steal me a Story" (1987). She played Lt. Guyla Cook in "Hard Copy" (1987), and as Kathleen Meacham, wife of a police chief played by John Mahoney in "H.E.L.P." (1990). She made guest appearances in three of the "Star Trek" spin-offs:  Flanagan guest-starred in several episodes of "Lost" as Eloise Hawking, a recurring character. She appeared in such films as "The Others" opposite Nicole Kidman, "The Divine Secrets of the Ya-Ya Sisterhood" as the eldest Teensy, and "Waking Ned". She appeared in television series and stage productions including the Emmy-nominated miniseries "Revelations", starring Bill Pullman and Natascha McElhone, and in "Transamerica", starring Felicity Huffman. From 2006 to 2008, she played Rose Caffee, the matriarch of an Irish-American Rhode Island family on the Showtime drama "Brotherhood". Flanagan appeared with Helen Mirren in "Some Mother's Son", written and directed by Terry George, as the militantly supportive mother of a Provisional Irish Republican Army hunger striker in 1981. Subsequently, she spoke at a memorial hosted by Sinn Féin at the Citywest Building in Dublin for Irish republicans and their kin who were killed during the latest episode of the Troubles in Northern Ireland. Flanagan and her late husband Garrett O'Connor, an Irish nationalist from Dublin, were known to host parties at their Hollywood Hills home for people in the Irish community. In July 2009, she joined Sinn Féin president Gerry Adams for a series of lectures across the US supporting Irish unity. In October 2011, she announced her support for Sinn Féin politician Martin McGuinness in his unsuccessful bid in Ireland's 2011 presidential election.