Sacramentalism
In this book, sacramentalism refers to the sense of the sacred or holy the nuns both experience and bring to their lives in the monastery. Though their lives do not offer satisfaction in the worldly sense of material possessions and fame, for them the truth of Christ coming to earth as a man elevates the ordinary and makes it sacred. This theme can be seen repeatedly in the focus and contentment the nuns bring to their daily duties, whether in cases like Sister Miriam bringing breakfast to Sister John in the infirmary and preparing it for her, or Sister Priscilla turning every act into a sacrament, including things like emptying a pencil sharpener. Even the resolution at the end of the book shows the completion of the idea of sacramentalism in Sister John's life, as she keeps the faith and returns to her duties.
Sacrifice
Nuns experience sacrifice on a daily basis. As part of their vows, the nuns take a vow of poverty and simplicity. Not only that, they sacrifice access to the outside world and its entertainments: cell phones, movies, television, and more. They do this to both to enter into Christ's sacrifices and to rid themselves of distractions from focusing on him. In a way, Sister John has her own sacrifice to make: her life, or her visions?
Suffering
This book is full of examples of suffering. Helen suffering the jibes of her classmates about her running abilities; the abused chickens in the cages of the poultry farm Helen and her grandfather went to, the suffering of the family whose teenage daughter was shot in the head, Sister Teresa slowly losing more and more of her memories. Sister John suffers from the bad migraines that accompany her visions; Helen suffers over her absentee drunk mother, her grandparents' passing away, and more. Yet the most important thread of suffering running through the book is the suffering of Christ on the cross as well as other saints like St. Therese of Lisieux, St. Teresa of Avila, and others. Constantly, the other nuns point her to Christ, who knew no peace and suffered agonies on the cross up till the bitter end. St. Teresa suffered agonies with her constant illness, but for her it was transformational--through it she grew closer in her relationship to God. Some of it is also self-inflicted, as in the case of the weekly Miserere, where the nuns undergo discipline in penance for themselves and those who can't or won't pray for themselves.
Loneliness/Isolation
Both Sister John and Sister Miriam experience isolation and loneliness. Sister John experiences it three times: growing up with her grandparents after having been abandoned by her mother, undergoing her period of drought where she does not experience God in the monastery, and while deciding what choice to make about her surgery. In the scenes where we see Helen as a child, the other children at school make fun of her. A sober, unhappy child, one of the most poignant scenes of the book is Helen, curled up in her room in the summer, dissatisfied and hurting after another brief, impersonal letter from her mother.
Sister Miriam is isolated from her family, who think she has joined a cult and is merely seeking attention. Tentative and thoughtful at the same time, she is seen by Sister John and the other nuns as a sort of bird. She talks to Sister John about feeling like she does not belong in the monastery, but after talking to Mother Emmanuel she realizes that the cost of following Christ might be higher than she realized, but she presses through anyway. The book ends with her taking temporary vows and leaving novice-hood behind.
Doubt
Every nun goes through periods of doubt, but those periods of doubt and darkness, Mother Emmanuel tells the nuns at Sister Miriam's ceremony, that teach them the power of faith and the light it gives off. Father Aaron also tells her that it is better to doubt the state of our soul than to assume we are all right with God. During her time of drought, she doubts her vocation, but still presses on. When she gets her diagnosis of epilepsy, Sister John seriously doubts the veracity of her faith and wonders if it had all been built on the illusion of a diseased mind (though the power of her faith does shine). Sister John's doubts, however, are doubts of herself--not of God. She realizes after meeting Dr. Sheppard the first time that she is so fortunate to know that God is real and that his love never fails.
Knowing God
One of the biggest themes of this book is the cost of knowing God. Sister John had come to the monastery because she wanted to know God, but during her period of drought she realizes that wanting to know God isn't the same thing as him giving into her every desire. So she struggles with her period of drought. The mystical visions are like rain to her, but as Father Aaron reminds her when she tells him about her diagnosis, he reminds her that loving God is about trusting herself to Him completely, not about what she can get out the relationship. The intense period of questioning and soul-searching Sister John undergoes after talking to Father Aaron is focused on her asking herself how truly she knows God. In the end, she realizes, it doesn't matter: her job is to follow him and love him and not, as Father Aaron taught her, to be in the relationship for the benefits.
Forgiveness
The theme of forgiveness shows particularly in Sister John's interactions with her mother. Growing up with only the occasional letter from her mother was very hard on Sister John/Helen and was part of the reason she joined the monastery: to be part of a community that was connected by Christ, not by blood. It would have been easy for Sister John not to forgive her mother, particularly after Sister John realizes that her mother was there not to start bridging the gap between them but rather to cut off connections completely. Nevertheless, her choice to forgive her mother, let the deception pass, and pray for her siblings reveals again that, with the visions or without, Sister John is a devout believer who practices her faith even in times of doubt.
