Homer Wells (Tobey Maguire), an orphan, is the film's protagonist. He grew up in an orphanage directed by Dr. Wilbur Larch (Michael Caine) after being 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 is also secretly an abortionist. Larch trains Homer in obstetrics and abortions as an apprentice, despite Homer never even having attended high school.
The film continues as Homer decides to leave the orphanage with Candy Kendall (Charlize Theron) and her boyfriend, Wally Worthington (Paul Rudd), a young couple who work at the Worthington family apple orchard. They had come to the clinic to have an abortion. Wally leaves to fight in World War II. While Wally is away, Homer and Candy have an affair. Later, Wally's plane is shot down and he is paralyzed from the waist down. When he returns home, Candy takes care of him and leaves Homer.
While he is away from the orphanage, Homer lives on the Worthington estate. He goes to work picking apples with Arthur Rose's (Delroy Lindo) team. Arthur and his team are migrant workers who are employed seasonally at the orchard by the Worthingtons. Mr. Rose impregnates his own daughter (Erykah Badu), and Homer, who disapproves of abortions, realizes that in Rose's case, he must perform one for her. Later, when Arthur makes another amorous advance toward his daughter, she stabs him, and as a last request, the dying Arthur asks the other workers to tell the police that his death was a suicide. Eventually Homer decides to return to the orphanage after Dr. Larch's death from inhaling an ether overdose, and works as the new director.
At the end of the film, Homer learns that Larch had faked Homer's medical record to keep him out of the war, and later made fake credentials for Homer in order to convince the board overseeing the orphanage to appoint him as the next director. Finally, Homer fills the paternal role that Larch previously held for the children of the orphanage.