Anna Leonowens part avec son fils Louis au Siam (aujourd'hui la Thaïlande) afin de devenir la gouvernante des enfants du roi Mongkut (Rama IV). Malheureusement, ce dernier refuse de lui donner la maison qu'il lui avait promise et l'oblige à vivre dans le palais. Mécontente, Anna décide de quitter le Siam, mais Lady Thiang, la première femme du souverain, la fait changer d'avis. Elle décide alors d'aider Mongkut qui prend l'habitude de la faire réveiller à des heures tardives pour lui poser des questions. Un ambassadeur d'Angleterre, sir Edward doit venir au Siam pour se rendre compte si le roi est réellement barbare. Avec l'aide d'Anna, le roi réussira à prouver que son pays est civilisé et offre une fête très réussie. Tout semble aller bien.
On the eighth of April of King Gyoeng-deok's 10th year of the reign of the Unified Silla Period, Guseulagi, a daughter of Yu Jong, joins the king's parade to Bulguksa Temple, where she meets a stonemason named Asadal from Buyeo. Having a crush on him, she visits Sakyamuni Pagoda, a masonic site; only to find that Asadal had broken down from exhaustion. While she takes care of him, her love for him grows. But Asadal misses his wife who is waiting for him in Buyeo. Meanwhile, Geum Seong who has a crush on Guseulagi, asks his father, Geum Ji, to propose on behalf of him. But Yu Jong is so dissatisfied with Geum Ji because he is a treacherous subject, that he turns down the proposal, instead of hurrying up his daughter's marriage with Gyeongsin, a faithful subject. Asanyeo who has been waiting for her husband Asadal in Buyeo goes to Bulguksa Temple after her father-in-law had died.
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.