The episodic, nearly plotless narrative of Death Comes for the Archbishop begins with a Prologue in which the Vatican assigns Father Jean Marie Latour, a French Jesuit missionary priest serving in Sandusky, Ohio, to the New Mexico territory following the region's annexation to the United States. Latour is elevated to bishop, and sets out for Santa Fe with Father Joseph Vaillant, a personal friend from the pair's schooldays.
Latour and Vaillant are charged with reinvigorating the Catholic Church in the region after nearly three centuries of neglect. Although the region can still be considered predominantly Catholic, the faith has been usurped by rogue priests who have taken mistresses with whom they have fathered children, abused the Mexican and Indian natives, and exhibited greed.
Latour sets out to impart a disciplined approach to Catholicism in the Southwest, meeting resistance from Padre Gallegos in Albuquerque, Padre Antonio Jose Martinez of Taos, and Padre Lucero of Arroyo Hondo. Gallegos is a hedonistic glutton and gambler, Martinez a promiscuous libertine, and Lucero a greedy liar.
It takes Latour nearly a year to travel from Ohio to New Mexico, traveling down the Mississippi River to New Orleans, and then on to Galveston by steamboat. He loses most of his possessions in Galveston, when the steamboat is wrecked, but continues to travel by land across Texas and into the New Mexico territory with a mare and a pack mule.
Upon arriving in Santa Fe, the Mexican priests refuse to acknowledge Latour's authority. In order to clarify the matter with the Archbishop of Durango, Latour sets out on a 3,000-mile journey. On his way, he gets lost. He is rescued by a little girl who leads him to Agua Secreta (Hidden Water). Here he learns that the priests of the region have charged exorbitant amounts to perform the Sacrament of Marriage, causing many of the natives to take wives without benefit of marriage. While admiring the craftsmanship and artistry of the native church, Latour recognizes that the natives have allowed their own superstitions to permeate their Catholic faith.
Latour returns to Santa Fe with documentation of his Vicarate, and finds that he has endeared himself to many of the town's residents as his presence has prompted some corrupt priests to resign their posts. Vaillant sets out for Santo Domingo and Albuquerque, in order to perform baptisms and marriages. The Indians of Santo Domingo, however, are suspicious of Latour due to the ill treatment they received from Spanish conquerors centuries ago. In Albuquerque, he meets Manuel Lujon, a wealthy landowner, with whom he barters for two mules.
While traveling to Mora together, Latour and Vaillant stop at a house to escape bitterly cold rain and to seek a warm place to rest. The house is inhabited by an older man and his young Mexican wife. The wife warns the two priests to leave as soon as possible because she fears her husband will kill them. When they arrive in Mora, they are followed by the woman. She tells the priests her name is Magdalena and her husband's name is Buck Scales. She reports that Buck killed four travelers on the Mora trail. Scales is subsequently arrested and hanged, and Kit Carson takes Magdalena to live with him and his wife near Taos.
Latour and his guide, Jacinto, travel west to the Indian missions. They spend time in Albuquerque with Padre Gallegos. Gallegos, afraid that Latour will ask him to accompany him on his visits to the West, wraps his foot in bandages and complains that he has gout. Latour and Jacinto push on to the pueblo of Isleta, where they meet Padre Jesus de Baca. The elderly priest lives in poverty among the Indians of the pueblo, claiming only one possession@ — a wooden parrot. He tells Latour that the Indians of Acoma own a portrait of St. Joseph that possesses the miraculous power to bring rain.
Latour earns the admiration and respect of Jacinto. He tells Latour the story of the elevated rock plateau of Acoma. Initially a sanctuary for Indians seeking shelter from other marauding tribes, a great church had been built in the sixteenth-century by the missionary Fray Juan Ramirez. On their return trip, Padre Jesus de Baca tells Latour the story of Friar Baltazar Montoya, a seventeenth-century priest of Acoma. Montoya virtually enslaved the Indians of Acoma, forcing the women to carry water daily up the side of the mountain to nourish his outlandish gardens. The Indians were afraid that Montoya might possess magical powers beyond the ability of the portrait of St. Joseph to bring rain.
Wishing others to admire his garden, Montoya plans a dinner party. He invites several missionaries. During a story by one of the priests, a serving boy becomes distracted and spills a platter of gravy on one of the guests. An angry and drunken Montoya throws a goblet at the boy, which kills him. The guests leave, and the Indians revolt against Montoya by throwing him from the plateau.
Latour returns to Santa Fe, and dismisses Father Gallegos. Vaillant replaces Gallegos, replacing his predecessor's revelry with a more austere devotion. Vaillant is dispatched to Las Vegas. On his way back to Albuquerque, he stops to administer Last Rites to residents of a Pecos Mountain village who are afflicted with black measles. Vaillant becomes afflicted as well. Latour travels to help his friend, and stops along the way to visit Jacinto, his wife Clara and the couple's sick child. Latour ponders the impact of white settlement among the Indians and the diseases the whites have spread.
Latour and Jacinto set out toward Vaillant but encounter a blizzard. They seek refuge in a cave that Jacinto confides has been used for Indian ceremonies. Jacinto beseeches Latour to never mention the cave to anyone@ — a request that Latour honors. The two weather the storm in the cave and find Vaillant the following day. Kit Carson is already there, and they take Vaillant back to Santa Fe.
Carson tells Latour about a white trader named Zeb Orchard. Orchard is a recluse, but Latour arranges a stay with him to learn more about Indian customs and ceremonies. Orchard belittles Indian customs, but Latour confesses that the Indians' veneration of customs and traditions is similar to the Catholic faith.
Latour and Jacinto travel to meet Padre Antonio Jose Martinez, the elderly priest of Taos. Informed by Kit Carson that all white men were distrusted in Taos, Latour also learns that Martinez is widely regarded as the instigator of an Indian revolt that resulted in the murder of more than a dozen white men, including the territorial governor. Seven Indians were hanged for the murder, but Martinez was never indicted. Instead, he convinced the Indians to sign over their worldly possessions to him before they were executed, resulting in Martinez becoming one of the wealthiest men in New Mexico.
Among the first things Latour learns upon meeting Martinez is that he has fathered children. Martinez challenges Latour on the Catholic Church's celibacy rule for priests. Martinez claims the native priests are more devout than the French Jesuits and warns Latour that enforcing "European formalities" will result in "infidels and profligates." He challenges Latour to dismiss him, saying he will form his own church.
Despite their disagreements, during High Mass the following day Latour admires Martinez's singing voice as well as the man's undeniable charisma. He discusses the matter of Martinez with Mrs. Kit Carson, who tells him that a disagreement with Martinez will set the Indians against Latour. He confides to Vaillant that he will replace Martinez eventually, but he will replace him with a Spanish priest when he returns from a trip to the Vatican in Rome.
Latour returns from Rome a year later with four French priests and one Spanish priest. He appoints the Spanish priest, Father Taladrid, to replace Martinez, allowing him the privilege to celebrate Mass upon Holy Days. When the arrangement proves untenable to Taladrid, Latour decides in favor of the Spanish priest. Martinez, infuriated, forms a schismatic church with Padre Marino Lucero of Arroyo Hondo. Lucero is depicted as an avaricious old man, given to castoff clothing and austere eating habits. In response, Latour sends Vaillant to strip Martinez and Lucero of the rights and privileges of the priesthood. Although excommunicated, the two priests continue their heretical schismatic church until their deaths shortly thereafter. While Martinez dies without repenting, Vaillant presides over Lucero's reconciliation with the Church. Upon his death, it is revealed that the miserly priest had saved nearly $20,000 in American money.
Latour becomes determined to build a cathedral in Santa Fe. He enlists the financial aid of Don Antonio Olivares, a wealthy Mexican rancher with Dona Isabella, his American wife from Kentucky who was raised as a Southern belle in Louisiana. The couple have a daughter, Inez, who possesses none of her mother's beauty but sings beautifully. At a New Year's party thrown by the Olivares, Don Olivares pledges enough money for Latour to build the cathedral. It is also where the character of Don Manuel Chavez is introduced to the reader. A master marksman, Chavez hunted Indians for sport as a young man. Surviving an Indian attack that killed all fifty of his companions, including his brother, Chavez walked sixty miles to the future location of Fort Defiance. A follower of Padre Martinez, Chavez distrusts Latour.
Olivares dies before bequeathing the promised cathedral monies to Latour. His death begins a prolonged legal battle between Dona Isabella and Olivares's brothers. The brothers claim that Inez is too old to be the daughter of Dona Isabella, which Dona Isabella will not refute for fear of revealing her age. Latour convinces her to reject her vanity for the greater purpose, and she consents. She eventually wins the lawsuit.
Following the Gadsden Purchase, which allowed the United States to annex areas of southern New Mexico and Arizona, Father Vaillant travels to Mexico to negotiate the establishment of parish boundaries in the area. On his return, he is stricken with malaria. Latour and Jacinto ride to Arizona, find Vaillant, and bring him back to Santa Fe to recuperate. It is the month of May, and Latour's orchard and garden are in full bloom. Vaillant welcomes the respite in Latour's garden as an opportunity to meditate on the Virgin Mary as he had done when assigned to the Great Lakes region of the Midwest. Vaillant considers May to be the month when all important events occur in his life.
Latour tells Vaillant he is eager for him to stay with him in Santa Fe. Vaillant responds that he hopes to be healthy enough for travel by July in order to educate Catholics who have lapsed in their practices. He equates the Indians with children who have no use for property or financial gain. He relates an anecdote of an Indian he has met who took him into a cave where his family had hidden items for performing a Catholic Mass. The Indian tells Vaillant that his family hid the items after the Catholic mission from where they were kept was attacked by Apaches. He believes the story of the artifacts is a parable of the Catholic faith being buried in the frontier waiting to be discovered. He convinces Latour that he must return to his missionary work. The priests' conversation is interrupted when Magdalena enters Latour's garden. Her appearance is accompanied by a flurry of pigeons and doves, and the priests are reminded of how much she has changed since they first met her.
The following December, Latour is feeling that his efforts are having no impact on the area. He wakes in the middle of the night to an early snowfall, and walks to the church. In front of the church is a weeping woman who Latour recognizes as Sada, a Mexican slave to a local Smith family, Protestants who publicly belittle and blaspheme the Catholic faith. The family refuses to allow Sada to practice her Catholicism, and she has escaped for the evening to pray in the chapel. Latour gives her his cloak to wear and allows her into the church, where she kisses the floor and prays with him. The experience allows Latour to see the importance of his mission: "The church was Sada's house, and he was a servant in it."
When spring arrives, Latour and Jacinto visit the Navajo Eusabio, who has recently lost a son. Latour uses the visit to reflect on his long friendship with Vaillant. Latour recognizes that Vaillant may have been a poorer student but was always more fervent in his faith. He recognizes that Vaillant is fond of good food and drink but nevertheless rigidly observes fasts. He also admires Vaillant's easy demeanor with new people. He remembers a story of Vaillant's audience with the Pope Gregory XVI. Instead of bringing the one customary item for the pope to bless, Vaillant brought two suitcases of items. He so delights the pope that the pontiff forgets several subsequent engagements.
Latour sends Jacinto to Arizona to deliver a letter to Vaillant. Eusabio accompanies Latour on his return to Santa Fe. During their travels, Latour notices that the Indian way is to not disturb the landscape whenever possible, whereas white men seem to assert themselves as much as possible.
Vaillant returns to Santa Fe at Latour's command but wonders why he has been there for three weeks with no reason being given. Latour takes his Vicar for a ride to show him the rock he has selected as the stone for the cathedral he plans to build. Vaillant is puzzled as to why Latour is so emphatic about the design of the cathedral and why he has been called back to Santa Fe.
Latour receives correspondence from the Bishop of Leavenworth, Kansas, that the Gold Rush of Colorado has created a need for a priest to serve the makeshift towns of tents and shacks that have cropped up near Pikes Peak. Informing Latour that the Colorado territory is under his domain, it is incumbent upon him to assign the priest. Latour tells Vaillant that he will fill the position. Although Vaillant is prepared to leave immediately, Latour orders him to stay until a custom wagon can be built and adequate provisions acquired. Vaillant reflects on a murderer he visited in Chimayo. The criminal was making a pair of boots for the patron saint of the Chimayo church. His parents would come for his execution and return home with the boots. Vaillant is certain the men to whom he'll administer in Colorado will be less devout.
Vaillant's wagon takes a month to build. Latour recognizes that the two will probably never work together again. Vaillant considers the opportunity to serve in Colorado an act of divine providence. Latour assures him that it was a coincidence, because he called Vaillant back from Arizona because of his loneliness. The Vicar leaves for Colorado, and the Bishop's loneliness is mitigated by his recognition of the presence of the Virgin Mary. He considers the wooden carving of Mary in the Santa Fe church, and the Mexican devotions to her in the form of clothing. He places their work on equal footing with Raphael and Titian, who also wardrobed the Virgin Mary in their art.
Latour's premonition that Vaillant would never return to work in New Mexico is proven correct. The Vicar returns to Santa Fe to recuperate from illnesses and to attend the formal proceedings marking Latour's elevation to Archbishop. Vaillant's life in Colorado is hard and cold, and he misses the mountains of the Southwest. He suffers permanent injury when his wagon falls into a ravine. His parishioners in Colorado, though far more wealthy, are less giving than the peasants of New Mexico, causing Vaillant to travel frequently to Santa Fe to raise money for his church in Colorado. When the residents of Santa Fe bestow ample gifts on Vaillant, Latour states that he'll need a cart to deliver his cargo to Colorado. The following morning, a cart is delivered. The two men say their goodbyes, with the Archbishop declaring the Vicar "a great harvester of souls, without pride and without shame."
The Archbishop spends his retirement years on an estate four miles north of Santa Fe. He bought the acreage before his retirement so that he could enjoy the orchard he planted. He also builds an adobe house and a chapel. As a retiree, Latour trains missionary priests. He spends much of his time gardening. He receives Bernard Ducrot, a young Seminarian who becomes a good friend to the Archbishop during his last years. He contracts a fever and begins to speak nothing but French. He asks the new Archbishop for permission to return to his study in Santa Fe, and his request is granted. When he returns to the city, he bemoans the number of wood-frame houses that have become more prominent. His cathedral has been built, and Latour observes the building by the light of the Southwest sunset.
Latour has come to love the New World more than the Old, and he prepares to die in his adopted homeland. Ducrot and Magdalena look after the Archbishop as his health continues to fail. He ponders the hardships of the missionaries in New Mexico, comparing them to the deprivations of St. Paul and other early Christians. He considers the hardships of the missionaries to be greater due to the greater distances they have traveled from their homelands.
Latour remembers a story another priest had told him about Father Junipero. Junipero had traveled with a companion across a vast desert, arriving at a monastery in good health with no provisions. The pair relates the story of the gracious hospitality of a young Mexican family consisting of a venerable man, his beautiful wife, an infant, and a pet lamb. Junipero and his companion eat well, sleep, and awaken to a table of food. The family, however, is gone. The brothers recognize the landmarks depicted by Junipero but have no recollection of a building or family living there. Latour recognizes the family in the story as the Holy Family and is charmed at the simplicity adopted by the Divine Family.
Latour's memories return to his decision to leave France for America with Vaillant. He remembers Vaillant faltering in his resolve and convincing his friend to travel as far as Paris. Latour's encouragement was the impetus Vaillant required to fulfill his pledge as a missionary in the New World. Latour marvels at his now-deceased friend's accomplishments despite his ill health and setbacks.
Among the setbacks faced by Vaillant is the interest due on loans for property he purchased for the Church. He is summoned to Rome to explain his complicated financial arrangements before a papal court. Vaillant returns to Colorado before he dies, and Latour travels to his funeral. Also attending the funeral is Father Revardy, who had served with Vaillant for more than twenty years. He is in Chicago when he hears of Vaillant's death, but he rushes back in ill health to attend the funeral of his friend. Revardy arrives halfway through the funeral and is immediately taken to the hospital afterward; he dies a few days later. Latour recalls that his friend inspired such devotion from men of all races.
Recognizing that he has outlived most of his oldest acquaintances, Latour is visited by Eusabio. Eusabio relates that he traveled to Santa Fe from Gallup in one day, whereas in the past it would have taken two weeks. Eusabio is not encouraged by the progress of civilization but is told by Latour that it is better to not know the future. When Eusabio leaves, Latour tells Bernard that he has seen two great wrongs righted in his lifetime: the end of slavery and the restoration of the Navajos to their rightful lands.
Latour's admiration for the nomadic Navajos is strong. He recognizes the injustices committed against them by white men and Apaches alike. He considers Kit Carson misguided for his role in eradicating the Navajos. Carson had found the Navajo's hidden fields located in a red-sandstone canyon and destroyed their corn fields and orchards. The act so disheartened the Navajos that that ceased to fight, and most of them were captured and relocated. Eusabio arranged a meeting between Latour and Manuelito, a Navajo leader. Manuelito is unable to convince Latour to intercede between the Navajos and the U.S. government, because Latour believes that a Protestant country will not accept a Roman Catholic priest's recommendations. The government changed its decision five years later, and the Navajos were allowed to return to their sacred lands.
During his last days, Latour sleeps often and eats little. His cathedral is full of parishioners who pray for him. On his deathbed, he returns to the day he convinced Vaillant to travel to Paris with him. Latour dies, and all of Santa Fe's Catholics pray for him. His body is laid before the high altar of the cathedral he built.