In an extremely rare decision, the Catholic Church officially recognized the demonic possession of the 19 year-old college freshman. Told in flashbacks, The Exorcism of Emily Rose chronicles the haunting trial of the priest accused of negligence resulting in the death of the young girl who is believed to be possessed and the lawyer who takes on the task of defending him.

Lawyer Erin Bruner (Laura Linney) takes on the church and the state when she fights in defense of a priest, Father Richard Moore (Tom Wilkinson) who performed an exorcism on a young woman, Emily Rose (Jennifer Carpenter). Bruner must battle the state lawyer as well as her own loneliness, as she realizes that her career so far has not fulfilled her. She takes the case, albeit reluctantly, because she believes it will elevate her to senior partner at her law firm. The priest agrees to let her defend him only if he is allowed to tell Emily's story

The trial begins with the calling of several medical experts by the prosecutor, Ethan Thomas (Campbell Scott). One expert testifies that Emily was suffering from both epilepsy and psychosis. The defense contests that she may have actually been possessed, though Bruner is careful never to say that in so many words intially. Indeed Bruner explains that Emily was suffering from something that neither medicine nor psychology could explain, and that Father Moore as well as her family realized this and tried to help in another way. Several flashbacks show how this began. Alone in her dorm room one night, at 3:00 AM, she smells a strange burning smell from the hallway. When she checks on it, she sees the door open and shut by itself several times. When she goes back to her room, she sees a jar of pencils and pens move by itself. Additionally, her covers roll themselves down, and a great weight seems to press down on her, a force which also proceeds to choke her and seemingly to possess her momentarily. Through these episodes she wonders if they are really happening or if it is just a hallucination she is experiencing. She suffers more "visions", is hospitalized, and diagnosed with epilepsy. She is given anti-seizure medications which she claims do not work. Her visions continue, as do her severe bodily contortions.