Dr. Iannis lives on the Greek island of Cephalonia with his daughter Pelagia. Pelagia has learned about medicine by observing her father. Pelagia meets a young fisherman named Mandras, and they become engaged. War has been declared, and Mandras decides to go fight at the front. Pelagia's letters to him go unanswered. Meanwhile, Carlo Guercio fights among the Italian forces that invade Albania, and sees his beloved friend, Francesco, with whom he is in love, shot by the Greek army.
In 1941, Italian and German soldiers are posted to Cephalonia, where they are ostracized by the locals. Pelagia is determined to hate them, especially when a young captain by the name of Antonio Corelli is domiciled with her. Mandras comes home from the war and Pelagia realizes she no longer loves him. Mandras leaves for the Greek mainland, where he joins the communist partisan organisation ELAS. ELAS is cruel towards the civilian population and more frequently attacks other partisan groups for being ideologically different than the Axis' occupying forces.
When Italy surrenders, their former German allies turn on them. After defeating the Italian division, the German soldiers on Cephalonia carry out a massive execution. Corelli's life is saved by Carlo Guercio, who shields him with his body when they face execution by firing squad. Guercio dies, and the wounded Corelli is aided by a Greek back to Pelagia's house. Corelli has to stay hidden from the Germans, whose orders are to kill any surviving Italians.
As soon as he is well enough, Corelli escapes to Italy, promising Pelagia that he will return as soon as the war ends and then they will be married. Corelli leaves Antonia, his mandolin, with Pelagia for safekeeping.
The war eventually ends and Communists take over the island. Dr Iannis is considered an intellectual, therefore suspect, and is sent to a camp along with some of his friends who protest against his treatment. Mandras returns, indoctrinated with Communist ideologies and having learned to read. He has read Pelagia's letters and knows that she does not love him, so he tries unsuccessfully to rape her. Mandras' mother realizes what almost happened and repudiates her own son. Ashamed, he commits suicide. Mandras' mother comforts Pelagia and for the remainder of her life, remains close with Pelagia.
Some time after, a baby girl is left on Pelagia's doorstep, whom Pelagia adopts. Dr Iannis comes home, traumatised. The baby girl, whom Pelagia has named Antonia, grows up and marries. Antonia later has a son who is named Iannis in honor of the doctor.
Many years later, Corelli, now a famous mandolin player, visits Pelagia one last time.
