The film follows the conflict between Frankie (Patricia Arquette), an atheist Pittsburgh hairdresser who exhibits true stigmata, and Father Andrew Kiernan (Gabriel Byrne), a former scientist and ordained Jesuit priest who, as part of the Congregation for the Causes of the Saints, investigates miracles for the Vatican. Kiernan soon discovers that the stigmata stems from the spirit of Father Paulo Alameida, who was excommunicated for his discovery of a lost Gospel challenging the very foundations of Catholicism by suggesting that Jesus Christ did not want churches built to worship God. When a powerful Vatican cleric, Cardinal Daniel Houseman (Jonathan Pryce), attempts to have Frankie silenced, she and Kiernan go on the run. The movie does not suggest that Jesus Christ did not want churches b