Sam Rizzo, a football star and class president of DuPont High, and his elder sister, Francine, a tough girl who likes to kickbox, enter the world as children of a premonition. Their single mother believes that she will die giving birth to Sam, and that is precisely what happens. Without a mother or father to care for them, they end up as foster children being reared by their Aunt Clara, a failed nun and the sister of their deceased mother. Clara must abandon God's call to enter a convent because she cannot overcome the sins of the flesh, although she tells everyone that she had to drop out of the novitiate to care for her dead sister's children.

Deep inside her, Clara harbors a regret and self-hatred so deep that it manifests in her determination to make something holy of Sam and Francine so that she can redeem her life and the life of her deceased sister. She is determined to send Sam to a monastery and send his sister to a convent. So she vows to do everything she can do to keep the boy and girl as pure virgins because she wants their call to a religious order to be free and clear of those sins of the flesh that sidetracked her.

As such, Like Trembling Birds traces Sam's and Francine's spiritual journey as they make their way toward the religious life of their aunt's choosing. However, what their abusive aunt does not realize is that God has other plans for these two. And although they must endure harsh treatment from manipulative Aunt Clara, in the end, each of them finds love. Francine falls in love with a girl she meets at work, and Sam falls in love with a girl who tries to ruin him but who then finds her rescuer in Sam. This story presents us with love amid the pain of loss and sorrow and then joy. The spiritual journey of each sibling does end in joy, but it's a joy that defies understanding and that blossoms only by the mysterious work of God.