Father Andrew Kiernan (Gabriel Byrne), a priest-scientist who works for the Vatican's Sacred Congregation for the Causes of Saints, is dispatched by Cardinal Houseman (Jonathan Pryce) to investigate a church in Brazil where a statue of the Virgin Mary has blood streaming from her eyes. This inexplicable event is somehow connected to the death of a priest who is translating a controversial gospel written in the first century, which could shake the authoritarian foundations of the Catholic Church.

When a thief steals the rosary from the dead priest's casket, an American tourist purchases this devotional artifact and sends it as a souvenir to her daughter Frankie Paige (Patricia Arquette), a hairdresser who lives alone in Pittsburgh, Pennsylvania. Soon after touching the rosary beads, this twenty-something woman finds herself in the hospital with deep puncture wounds in each wrist. Her story is picked up by the media when her back is lashed by an unseen force while she is on a subway train. Father Kiernan, who is sent to investigate, tells Frankie that she is receiving stigmata, the five wounds suffered by Jesus when he was crucified. Unlike Saint Francis of Assisi and Padre Pio who were devout Christians experiencing this phenomenon, Frankie is a nonbeliever.

This supernatural thriller directed by Rupert Wainwright is very difficult to watch with its hallucinatory visual style and its surreal depiction of urban life. Those looking for a thrill-me successor to The Exorcist will be disappointed. The crux of the drama focuses on a Vatican conspiracy to suppress an Aramaic text, similar in content to the Gospel of Saint Thomas, where Jesus talks about the direct experience of the Kingdom of God without any need for the authority or structures of the institutional church.