Homer Wells, an orphan, grows up in a Maine orphanage directed by kindly, avuncular Dr. Wilbur Larch. Homer is returned twice by foster parents; his first foster parents thought he was too quiet and the second parents beat him. Dr. Larch is addicted to ether and also secretly performs abortions for women. Conditions at the orphanage are spartan, but the children are treated with love and respect, and they are like an extended family. Each night before they go to sleep, Dr. Larch says to the boys, "Goodnight you Princes of Maine, you Kings of New England", as both encouragement and a kind of blessing.Homer, the oldest among the orphans, is very bright, helpful and even-tempered, so Larch trains him in obstetrics and abortions as an apprentice, despite Homer's never having attended high school. Homer disapproves of abortions, and, although he has been trained by Larch in the field, he refuses to perform them. After several years, Homer is very skillful and confident in performing obstetrical duties. Larch wants him to take over his position after he retires, but Homer finds this idea impossible, because he lacks formal medical education and wants to see more of the world than just the orphanage.Homer leaves the orphanage with Candy Kendall and her boyfriend, Wally Worthington, a young couple who came to the clinic to have an abortion. Wally is a pilot on leave from the service. Wally's mother, Olive, owns the Worthington family apple orchard where Homer settles in as a worker. Homer lives on the Worthington estate in a bunkhouse called the Cider House. Wally leaves to fight in World War II. Homer is exempt from military service because Dr. Larch has diagnosed that he has a heart condition.While Wally is away, Homer and Candy have an affair. He goes to work picking apples with Arthur Rose's team. Arthur and his team are migrant workers who are employed seasonally at the orchard by the Worthingtons, but are illiterate. When Homer reads them the rules of the Cider House that have been posted, the workers observe that the rules have been made without the occupants' consent by people who do not live there and so do not face their problems. Consequently, they feel that they can ignore these rules. Homer and Candy become much closer during this period of harvest and spend more time together while Wally is in Burma fighting.After Arthur and his team come back to work at the orchard the following season, it comes to light that he has raped and impregnated his own daughter, Rose. Rose confides in Homer after he finds out himself that she is pregnant and experiencing morning sickness. Homer decides that he must help Rose, and agrees to perform an abortion, with Arthur's assistance. A few days later, when Rose tries to run away, her father notices and goes to say goodbye; Rose stabs him and flees. Arthur then makes his own injury worse, and as a last request, asks Homer and another worker to tell the police that his death was a suicide.Wally returns from Burma a paraplegic, and although she loves Homer, Candy decides to go where she is most needed. Immediately following this decision, Homer learns that Dr. Larch has succumbed to (what he is told was) an accidental ether overdose. Eventually, Homer decides he too should go where he is most needed and returns to the orphanage, where he is greeted joyously by both the children and staff. Homer learns that Larch faked his diagnosis and medical record to keep him out of the war. Larch fabricated college credentials for Homer and used reverse psychology to convince the orphanage board to appoint Homer as the next director. Homer fills the paternal role that Larch previously held for the children of the orphanage, saying, "Goodnight you princes of Maine, you kings of New England".