Song of the Magdalene is Napoli's first young adult novel that uses the Bible as its source. Set in first-century Palestine, it recounts the adolescent years of Miriam, daughter of a prosperous and highly respected Magdala widower, and her struggle to remain true to her own ideals and passionate personality while trying to conform to the role of proper Jewess in a restrictive religious society whose stringent traditions hamper her every activity. The person with whom she had most in common is Abraham, the crippled son of the family's servant Hannah, who although bound by his paralysis, is free to think, read, and reason within the broken shell of his body.

It is Abraham who teaches Miriam to read and sing, who encourages her to grow intellectually and spiritually. The onset of her own seizures fills her with fear that she may be beset by unclean demons, but this dread is stilled when Abraham argues that to be handicapped is not a judgment by the Creator, rather it is a happenstance of cruel Nature. The tomboy and the cripple become two young rebels who unite to overcome all obstacles. Strong and lithe, Miriam uses a handcart to pull Abraham at first into the fields and then into the town so that he can experience the world around them. They do so with the grudging approval of Miriam's father and Abraham's mother who fear the possible consequences of their behavior.

Their household is joined by an unexpected ally when Judith—a barren widow who has wanted to marry Miriam's father ever since the death of his wife and her husband—seeks out Miriam after the girl has shamed her orthodox community by being inspired to sing aloud from the "Song of Solomon" in the House of Prayer, an act anathema for a woman, whose inferior sex is never supposed to speak aloud in the synagogue, or be taught to read, even from the Bible.

Miriam and Abraham eventually become lovers and consecrate their love in a marriage prayer to the Creator. Their union results in Miriam's pregnancy, despite Abraham's weakened condition after he has been exposed to the elements in one of their excursions into the fields. Now, it is Judith who gives Miriam support. After Abraham dies, Miriam and Judith prepare together for the child's birth, a child that Miriam longs for as a healthy extension of his father's spirit, a child whom Judith prepares to vicariously receive as her own. When the child is stillborn after Miriam's brutal rape by a Magdala carpenter, Miriam is sent to live with an uncle to quiet the vicious rumors spread by Jacob the carpenter that she has prostituted herself.

After a difficult sojourn with her relatives, Miriam sets off on a symbolic cleansing journey into deserted Qumran, the community of the Essene caves, where she prepares for her final journey toward the Messiah Joshua. It is here that she is first seen in the New Testament as the woman with seven unclean spirits, a link Napoli makes as she recounts the seven epileptic attacks that plague Miriam over the course of the book. That woman emerges as Mary Magdalene who carries with her always an alabaster jar of ointment and a song to sing for the many souls that yearn to be healed.