James Carroll sketches the struggle with his father, Joseph, in this autobiographical work that he subtitles, "God, My Father and the War that Came Between Us." James opens his story at age twenty-six, the day after his ordination as Father James Carroll. The Roman Catholic priest is celebrating his first Mass and preaching his first sermon. James' ordination gives him the strength to overcome his own silence and cowardice. Joseph Carroll is a domineering, Irish-American, traditional Roman Catholic father of five sons. He is a lawyer, successful FBI agent, Air Force Lieutenant-General in charge of enemy counts and targets for the Vietnam War and feels guilty from the Irish curse of his own failed attempt at becoming a priest.

The first chapter theme and title draws on a scriptural quote from Ezekiel that refers to a valley full of dry bones. Father James uses dry bones to describe the destruction his father and fellow generals cause by dropping napalm bombs on the Vietnamese people. Father James preaches a public, veiled condemnation of his father and his assembled comrades in arms. James, the author, but no longer Father, recounts the life and career of his father, Joe, and mother, Mary, from Irish Bridgeport to the FBI and their Washington success in the second chapter. James and his four brothers are born into privilege in Washington, D.C. As young boys they attend presidential inaugurations from 1945, on and see their father become the youngest Air Force general at thirty-seven. By 1958, the Carroll family is in Germany where the General's rank paves their way to Roman Catholic elites, Cardinals and the Pope. James recalls this as the best of times despite his struggles with adolescent sexuality and choice of career or calling. The Pope confirms his call to the priesthood. James confides that choice to his father in the fifth chapter he calls joy to his youth.

James' religious education begins in the sixth chapter when he enters seminary with the Paulists in 1963, graduates and is ordained in 1969. While in seminary, he develops his second and continuing vocation as a writer. His calling by progressive Pope John XXIII initiates a religious revolution that conflicts with his father's traditional Irish Catholicism. Joseph Carroll, the FBI agent, chases criminals and draft dodgers and as General chases Communists, despite Pope John's call to communicate with them. James' meeting with Robert F. Kennedy commits his interest and efforts to civil rights, but Joseph conspires to destroy Martin Luther King, Jr. The young seminarian takes the manner and style of the Negro slave that cuts capers in chains. James is silent about his beliefs when he is with his father. Their final conflict develops when Pope Paul VI preaches peace at the United Nations in 1965. James commits to the antiwar movement in direct conflict with Joseph.

James recounts his ordination as Father James Carroll in the ninth chapter and reflects on his first blessing and ritual imposition of hands on his parents and pre-ordination meeting with Tate, the hero of his writing career. The next chapter outlines his first assignment as a priest and development as an activist, radical priest and underground supporter. The last word in the eleventh chapter is Mary, the name of Joseph's wife and their mother. He is sick and dying with Alzheimer's disease. The family comes together at his deathbed to watch and commemorate a man they honor, love and respect despite their differences.