Shadow War in Crete begins in a maternity ward in New Jersey, where Amalia, a young woman of Greek heritage, is awakening from anaesthetic after giving birth to a stillbon child - or so she is told. When she learns that her husband, a young German doctor, has dissapeared as well, she decides to return to Crete to live with her parents.

The year is 1939, and Amalia's quest for inner piece soon becomes a struggle for survival as Greece is engulfed in World War II. Amalia's story becomes entwined with intelligence agents and the guerrillas - Greeks, British and Anzacs who hid in mountain caves, descenting at night to wreak havoc on the Nazis who occupied Crete for four years.