The story of Clock Tower 3 is set in London in 2003. Alyssa Hamilton is a 14-year-old girl who has been living at a boarding school for three years. Her mother, Nancy, sent her there after her grandfather, Dick, disappeared. The game begins with Alyssa receiving a letter from her mother telling her to go into hiding until after her fifteenth birthday. Alarmed, Alyssa decides to go against her mother's wishes and return home. However, when she arrives at the boarding house in which they live, her mother is absent, and the only person there is a man called "The Dark Gentleman". Determined to find her mother, Alyssa explores her mother's room. Suddenly, Frédéric Chopin's Fantaisie-Impromptu begins to play with no apparent source, and Alyssa is transported back in time to the streets of London during World War II.
