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The plot begins in 11th-century England, much knowledge having been lost in the Dark Ages, and the Church is fighting against black magic. The medical knowledge of Greek physicians like Hippocrates and Galen had been lost to the medicine of medieval Europe, until taught later in schools such as the School of Salerno (after the Arabic-Latin translation movement of the 12th century). In 11th-century England, travelling barber surgeons attempted to supply medical care to the ordinary population, often at the risk of the Church persecuting them for witchcraft.

Robert Cole has an extraordinary gift, where he can sense when someone left untreated has a terminal illness. He notices this for the first time when he feels as a little boy that his sick mother will die of appendicitis, a disease he was unaware of. The young orphan joins an itinerant barber-surgeon who calls himself Barber. Barber teaches him the basics of medieval medicine, with services such as cupping therapy, bloodletting, and dental extraction. Even as an apprentice Rob recognizes the limitations of these simple practices. When Barber suffers from a cataract, Rob consults a real Medicus for him. This Jewish doctor heals Barber completely. He learns a little bit of Jewish culture. He speaks with two children, Jesse and Benjamin. There, Rob sees for the first time a world map, and learns of the famous Ibn Sina, who teaches medicine in distant Persia. So he decides to train there to become a physician. During the Islamic Golden Age, the medicine in the medieval Islamic world (evolved from a symbiosis of Gondishapur Iranian medicine and Nestorian Byzantine medicine in Baghdad's House of Wisdom) is far more advanced than in Europe. The doctor, scientist and philosopher Ibn Sina teaches in Isfahan, the most important school for aspiring practitioners in the world at that time.

Rob discovers that Christians are forbidden in Muslim lands while Jews are tolerated. Upon arriving in Egypt, Rob, even though he is a baptized Christian, performs a circumcision on himself and calls himself Jesse Ben Benjamin, pretending to be a Jew. In a caravan he comes to know Rebecca who reads to him from a book about Aladdin and Sinbad the Sailor. He experiences a desert storm and almost dies. He suffers a concussion when he asks for admission to the school of Ibn Sina, by the Guardian, so that he is taken as a patient.

In a Bimaristan hospital and Madrasa college, he learns from Ibn Sina the basics of scientific medicine as well as other sciences and philosophy (including Aristotelian and Islamic philosophy). So Rob learns to perform a medical history and medical examination including pulse diagnosis, the leech treatment, the use of opium, including the analgesic effect, and surgical procedures. When a plague breaks out in the city and thousands die, the doctors remain at the patients' side. With the discovery of basic hygienic principles, the plague is overcome. Rob suggests that oriental rat fleas may be the carriers of the Black Death, and with rat poison the pest may be suppressed. The passion for Rebecca flares up again, as Rob takes care for the abandoned, sick of the plague, and nurses her healthy. There is extramarital sex between Rob and Rebecca that results in pregnancy. Adultery leads to the preparation of a stoning. Rob learns from the Shah on the burden of ruling.

The Christian, Jewish and Islamic religions are used in the evaluation of medical science. A conflict is sparked by the ethical assessment of the autopsy on the human body. As a Zoroastrian dies of appendicitis, Rob learns from him that he does not require the dead body in his religion. With him, Rob secretly performs an autopsy to deepen his knowledge of anatomy and to discover the inflamed vermiform appendix. Later, he is able to perform an appendectomy under anesthesia on the Shah.

Isfahan is betrayed by mullahs to the Seljuks to drive the Jews and secular blasphemers like Ibn Sina out of town or kill them. After a crowd destroyed the hospital and killed the employees, Ibn Sina commits suicide. Shortly before his death, Ibn Sina transfers his medical writings to Rob Cole in the burning library. Rob Cole may call himself 'Hakim,' an honorary medical title, which is given to him by the medical grandmaster.

After the death of Ibn Sina, Rob Cole returns with Rebecca as his wife back to London, to found a hospital. The old Barber, Cole's first teacher, learns from a little boy by the return of his former pupil and of its fame.

The Physician is a 2013 adventure movie with a runtime of 2 hours and 30 minutes. It has received mostly positive reviews from critics and viewers, who have given it an IMDb score of 7.2.