Deep in the Valley interlaces a story of young romance set in Yanaka (part of old downtown Tokyo) with a Japanese period drama based on Five-Story Pagoda, a classic literary work by Rohan Koda.
In the contemporary story, Kaori, a young woman working for a non-profit organization that restores home movies, learns that there used to be a five-story pagoda in the middle of Yanaka Cemetery. It burned down in 1957, and rumor has it that someone has an 8mm film of the fire.
Kaori visits Buddhist monks, a cemetery caretaker, a local historian, and traditional craftsmen in her search for the film. She falls in love with Hisaki, a local street punk, and together they discover the mysteries of the lost pagoda.
In a story set in the Edo period (18th century), Jubei, a young, obscure carpenter, aspires to build the Five-Story Pagoda alone despite the opposition of his boss, his colleagues, and his wife.
Mixing fiction and documentary, the film breaks the barrier dividing generations and fills the void of lost memories.