Filomena is the wife of the miller, Malaquias. She is miserable with labor pains and has been bedridden for three days. Her childbirth is failing to progress, and death seems likely for both mother and baby. A tiny hand protrudes from Filomena's vagina signifying the stalled process of birth and the urgent need for medical assistance. The midwife in this Portuguese village is not capable of performing such a difficult delivery. The local doctor is ill. He advises Malaquias to fetch a physician from another town but the cost is too great.

The Catholic priest, Father Gusmao, makes a nocturnal procession carrying the Holy Eucharist to the miller's home. He intends to administer Communion and Last Rights to Filomena. The priest examines her and discovers that Filomena's baby is in the breech position. He has little choice but to attempt delivering the baby by himself. Although Father Gusmao read a medical manual long ago, it is primarily intuition that steers his daring act. First a foot, then the body, and finally the head of a baby boy emerge from the birth canal. Mother and child survive. All the while, the Holy Eucharist in a pyx sits on top of a chest of clothes near Filomena's bed witnessing (or perhaps guiding) the entire sequence of events.