Shore has a specialty in the Roman Catholic Church: investigating miracles for authenticity and candidates for sainthood. Throughout the film we learn more about the case that made him drop out of the priest business. A priest, Father Falcone, had a reputation for being a healer. Shore found testimony from Jewish doctor who said the man had healed tumors, but further investigation uncovered heretical papers and Falcone’s death by suicide. He was no longer a candidate for sainthood, and many people found their faith crushed -- Shore’s faith along with Falcone's followers.
So he hesitates before taking the case of woman named Helen, recently deceased, who people are advocating for sainthood. Helen, though not a nun, lived in a convent. When she died, a statue of the Virgin Mary near her room began to bleed, and a young girl praying to that statue was cured of terminal lupus. If these miracles proved to be true, Helen might become an American saint (though the film was made in Canada).
During his investigation, Father Frank meets Roxane (Anne Heche), Helen's daughter, and begins an affair with her. He tells her about his decision to become a priest, based on a deal he’d made with God. If his father was healed, he would become a priest. His father's health improved and so Frank went to seminary and took his vows. Immediately after he took his vows, his father died. He felt God cheated him.
Father Frank begins to believe in Helen and fights the Vatican bureaucracy that doesn't look fondly on the idea of American saint. (The Archbishop of the Common Cause of Saints isn't fond of America in general. He admits he's heard there is a passable restaurant in San Francisco, but otherwise...) The Archbishop wonders why, if Helen was a true saint, God would entrust her case to someone like Father Frank?
The miracles of the statue and the healing would count for two of the three miracles needed for sainthood. Father Frank searches for a third. Eventually, he finds clues that there may have been a third miracle in Helen's childhood. During World War II, she prayed when bombs were dropped over her city; the bombs turned into pigeons.
He doesn't convince the Vatican mucky-mucks, but Father Frank finds his faith again. That’s swell, I suppose, but the whole procedure of a trial process to ratify saints (as portrayed in the film) looks rather silly to me, which is why I'm giving Father Frank and the church in the film just Two Steeples.