San Manuel Bueno, Martyr is a story about the life of one unusual priest named Don Manuel. What makes him so unusual? Well, he may be the only priest in the world who doesn’t believe in God. He agrees with the statement that religion is the opium of the people, and he feels burdened with his responsibility of being the one who administers this opium.
Most of the story is told from the perspective of Angela Carballino, a woman around fifty years old who wants to record the memories of her early years. In her confessional memoir, she reveals that Don Manuel, the great man who had loved helping other people, had lived a life full of spiritual turmoil himself.
As a child, Angela was raised by a deeply religious woman, and she was taught to be obedient and to love God. When Angela meets Don Manuel, she realizes immediately that the man is not like other people—he holds a special, important role as the spiritual anchor for the villagers, a role that he successfully fulfills. Don Manuel is beloved by everyone in the village, as he works hard to mend broken families, heal the sick, and clothe the poor. Angela soon develops a close bond with Don Manuel, coming frequently to confessionals and talking to him about all her worries and doubts.
Angela also has a brother, Lazaro, who spends many years living in the New World. When Lazaro comes home, he is dismayed by what he sees as his family’s backward, rural lifestyle, and tries to convince his mother to move the family to a big city. However, their mother angrily refuses to leave; she is too attached to her village, and to Don Manuel.
There was one more important thing about Lazaro: he doesn’t believe in God, and believes all religious officials to be corrupt and wicked. However, even Lazaro cannot help but admire Don Manuel’s kind spirit upon meeting him. The turning point for Lazaro comes when his and Angela’s mother becomes deathly ill. On his mother’s deathbed, Lazaro is moved by Don Manuel to promise that he will pray for her. This experience brings Lazaro and Don Manuel close together, and soon Lazaro enters the parish under Don Manuel.
Then, Lazaro becomes closer to Don Manuel, and the priest tells him his deepest secret: he also doesn’t believe in God. Furthermore, he believes that religion is a lie meant to disguise a terrible truth: humans are born for no other reason than to die. Finding common ground in this belief, the two men grow even closer. Angela is horrified when she discovers this shared belief. However, through conversations with Don Manuel and Lazaro, she grows to accept that it is necessary that the villagers of Valverde de Lucerna never discover this truth about Don Manuel.
In the epilogue of the story, it is revealed that this memoir is being read to us not by Angela herself, but a different, separate narrator. This narrator, who could be Miguel de Unamuno or a different person altogether, claims that they believe Angela Carballino’s account to be true, and that even if nothing is resolved through this memoir, they hope that the story will persist and endure throughout the world and “in the divine novel of our existence.”