Dr. Iannis owns a practice on the island of Cephallonia in Greece where he lives with his daughter Pelagia. He's a widower, his wife having died of tuberculosis years ago when Pelagia was a child. The two live happily together, and the doctor is training his daughter to take over his practice someday. Quick-witted and impulsive, Pelagia is determined to make her own way in life despite the misogyny of her time. The story is set during the reign of Benito Mussolini, right at the outset of WWII. When she meets a handsome fisherman named Mandras, she decides to marry him, but he is drafted to fight the Germans.
In the war readers are introduced to a character named Carlo Guercio who has his own plot line. He's an Italian who is fighting to capture Albania. Guercio has a difficult time in the war and witnesses some brutal events, including the death of his longtime friend Francesco at the hand of the Greeks. Due to the Italian military's insufficiency, the Germans arrive and conquer Greece. They deligate their control of Greece to Italy, however. Guercio ends up living in Greece where he's stationed temporarily.
As Italian soldiers start rolling into her town, Pelagia becomes increasingly disgusted by them. She's been writing Mandras daily but has never received a single response. The Greek citizens are ordered to board soldiers in their homes, and a Captain Antonio Corelli is sent to Dr. Iannis' house. Pelagia determines to hate him, but Corelli makes this difficult for her. He's a polite, good-humored young man with integrity and astounding skill on the mandolin. He entertains her with many performances on his mandolin, which he calls Antonia. Around this time Mandras is sent home from the war on injury leave. While Pelagia nurses him, she comes to realize that she doesn't love him and no longer desires to marry him. He confesses that he never learned to read which is why he never wrote her back. When Pelagia breaks up with him after he's well, Mandras despairs and leaves to join the underground movement. She's certain he'll die. In his absence, Pelagia finds herself slowly falling for Captain Corelli.
Mussolini is deposed in 1945, and Italy joins the Allied Forces. This means Corelli is free to return home to Italy, but his unit and most others decide to stay and fight the Germans in Greece. No match to the superior German forces, they are soon conquered and sentenced to death. Exploring every hiding hole on the island, the German troops track down every last soldier. When Corelli is captured and standing before a firing squad, he's miraculously rescued by Guercio who jumps in front of him for no apparent reason. Guercio sacrifices his life for a stranger. Pelagia manages to hide Corelli in her home until he's recovered from his wound and escapes to Italy.
As the war winds down, it becomes more and more gruesome. The Germans are outraged over their impending defeat and begin sending the locals from Cephallonia to camps in Germany. Dr. Iannis is taken and sent to a camp, so Pelagia lives alone. One day Mandras visits Pelagia. Indoctrinated by the Communists, he's come to confront her. They taught him to read, so he read all her war letters and learned that she had never loved him. He becomes irate when she denies this and attempts to rape her, but she fights him off. Mandras leaves, but he cannot live with what he's done and commits suicide.
Someone leaves a baby girl outside Pelagia's door suddenly. Seeing no other alternative, she decides to raise the child herself and names it Antonia. Eventually her father returns although he's never the same after his imprisonment. He dies in 1953 during a massive earthquake, so now it's just the two girls. Antonia grows up and gets married. Finally, decades later, Corelli returns. He's made a name for himself as a mandolin player and made peace with everything that happened during the war. When she asks why he didn't write to her all those years, she accuses him of forgetting. He explains that he returned to her decades earlier but just in time to see her raising Antonia and concluded she must've married someone else. Jealous and furious, he couldn't bring himself to knock on the door. The two resume their friendship in the end.
