The Conflict between Native Religion and Catholicism
As Father Latour gets to know his New Mexico diocese and tries to strengthen the Catholic faith among the Mexicans and Indians there, he finds himself in some conflict with the native beliefs, which are still very strong there. When he meets Padre Martinez, who preaches a very unorthodox Catholicism that takes on many native elements, he confronts the opposing vision of how Catholicism should work with existing views. As the Mexican priest tells him:
You know nothing about Indians or Mexicans. If you try to introduce European civilization here and change our old ways, to interfere with the secret dances of the Indians, let us say, or abolish the bloody rites of the Penitentes, I foretell an early death for you. I advise you to study our native traditions before you begin your reforms. You are among barbarous people, my Frenchman, between two savage races. The dark things forbidden by your Church are a part of Indian religion. You cannot introduce French fashions here (148).
Nevertheless, Father Latour has the sense that Padre Martinez is only able to carry on with his syncretic kind of Catholicism because of his cult of personality, and that historical progress will inevitably lead to the victory of the orthodox position.
Intimate Male Friendship, or Homosexuality
Willa Cather, who was known for her homosexual relationships and resistance to gender norms, illustrates in the case of Father Latour and Father Vaillant a relationship between two males that is intimate to the point of homosexuality; the trope of boon friendship and the Catholic priests' vows of celibacy, however, preclude the possibility of an openly romantic or erotic relationship, and thus presumably conceal the homosexual aspect from Cather's contemporaries, some of whom may have objected to it. Moreover, this obscurity of the exact nature of their intense friendship allows for Cather to paint the picture of emotional bonds with great understatement, such that the moment when Father Vaillant sheds a tear just before leaving, just as the time later when Father Latour thinks of his friend's departure, becomes imbued with great human feeling despite the fact that it is not so explicitly dramatic.
Ascetic versus Libertine Ways of Living
Part and parcel of Father Latour and Father Vaillant's work as missionaries to promulgate the Catholic faith is their personal necessity to maintain a highly moral way of living, which is meant to serve as a mark of their discipline and devotion to God. As leaders of spiritual communities who, especially in New Mexico, must struggle under harsh conditions to maintain their ways of life and connection with the divine, they understand their roles as exemplars. This kind of moral cleanliness is contrasted with the attitudes of some of the Mexican Christians, who are much more given to dramatic shows of faith, such as the Penitentes' practices of crucifying or scourging themselves, or the lax lifestyles of such priests as Padre Gallegos and Padre Martinez, for whom positions as leaders involve much more worldly power.
Narrating to a Friend
A substantial amount of the story is told not just by the narrator but also from one character to another. Father Latour often writes letters to such people back in Europe as Philomene, though it is most of all with his friend Father Vaillant that he shares stories of interesting events he has seen or heard of. Even though it never becomes the case that the entire narrative is understood to be told by a character, there is the constant pervading sense that Cather's narrative universe is made up of stories exchanged among people -- especially among friends. After Father Vaillant dies, Father Latour's storytelling tradition continues with the stories Bernard Ducrot has heard of him and the stories he tells the French priests he has gathered about him.
Life on the road
Since the missionary priests must frequently travel from one place to another to reach isolated religious communities and provide them with services and thereby a connection to the wider Catholic Church, a great deal of the novel either takes place on the road or mentions that the characters have been moving about. This significance of travelling is especially important to Father Latour and Father Vaillant's friendship, since the former, though he also travels often (such as to important religious councils), is strongly attached to the seat of his diocese in Santa Fe, whereas the latter, as Vicar General, is required to and enthusiastic to go wherever he is needed. Eventually, this leads to Father Vaillant's separation from Father Latour when he leaves to answer the call for help in Colorado.
Earthly vitality of New Mexico
Both Bishop Ferrand (in the meeting in Rome in the prologue) and Bishop Latour (in the final chapter, when he as returned to his native France) feel themselves, after years of work in the harsh and partly uncivilized environments and societies of the New World, to be strangers to the highly civilized and educated worlds they were brought up in. For Father Latour, the New Mexican landscape that once was so alienating to him has transformed in feeling to something very invigorating: he feels young when he wakes up in New Mexico, since it seems to be a recurrence of his youthful efforts when he was starting out as bishop.
Planting a garden
Opposed to a life of traveling and working as a missionary is the life of settling down into a community and establishing oneself with a household. Just as important as confirming his position as bishop and taking a place in his church for Father Latour is his planting a fruit in the garden of his bishop's residence, as it is later on, after his retirement, in cultivating the orchards of the country estate he buys. Even where his work as bishop and his personal spiritual devotions take up much of his time, it is still of great importance to Father Latour to be connected with the earth and the environment in which he lives.