Texas 1995, at the home of Madalyn Murray O'Hair (Melissa Leo), the founder of American Atheists, her son Garth (Michael Chernus), and her granddaughter, Robin (Juno Temple), the family is missing. Food is spilled everywhere, the door is unlocked, and Madalyn's dogs, which she takes with her everywhere, are running loose. The O'Hairs' friend, Roy Collier (Brandon Mychal Smith) arrives to discover they are missing and calls the police. The O'Hairs are in a motel room being held hostage by David Waters (Josh Lucas), a former employee at American Atheists, who wants to extort money from the O'Hairs. The scene cuts from The O'Hairs and their captors in 1995, to the investigation trying to find the family, and to the past. In 1955 Baltimore, Madalyn is a single mother, living with her son, Bill, and her parents. Madalyn announces that she is pregnant with her second child, which makes her father upset. Madalyn and Bill take part in an anti-segregation march and appear on the local news. In the 1960s, Madalyn, Bill and her second son, Jon become well known after they lead a campaign to abolish prayer from public schools, stating that it is unconstitutional. Madalyn becomes well-known around the country and starts to receive hate mail and death threats for her activism, as well as support and money from others as well. Madalyn starts American Atheists organization and appears on the cover of "Look Magazine" as "The Most Hated Woman in America"! In 1969, has a new husband, Richard, Bill (Vincent Kartheiser) is also married and has a daughter named Robin. After the family leaves a radio station where Madalyn is giving a interview, she is shot by a protester, but escapes with minor injuries. Madalyn makes regular appearances on talk shows like Tonight Show With Johnny Carson and Donahue. On the Donahue show she meets Bob Harrington (Peter Fonda), an evangelist minister and the two stage several more debates which make both them lots of money. Bill has a serious drinking problem which leads him to divorce his wife and Madalyn becomes the full guardian of Robin. Bill, eventually leaves his mother and atheism behind and becomes a Christian though Alcoholics Anonymous . In the present, when Bill learns that his mother, brother, and daughter are missing, he assumes it is one of Madalyn's publicity stunts, because she has "gone missing" before and has turned up safe and unharmed. In the early 1990s, Madalyn hires David Waters to the position of office manager, but he is soon discovered to have a criminal history, has a falling out with Madalyn and vows revenge. In 1998, David and his associates all openly admit to killing Madalyn and burying their bodies in the woods. After their bodies are found and buried in a cemetery. Roy and Bill visit Madalyn's grave. Bill says he doesn't want to pray because "that's what she would have wanted".
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