The story of two Catholic missionaries (Andrew Garfield and Adam Driver) who face the ultimate test of faith when they travel to Japan in search of their missing mentor (Liam Neeson) - at a time when Catholicism was outlawed and their presence forbidden.

As a young girl in Japan, Nagiko's father paints characters on her face, and her aunt reads to her from "The Pillow Book", the diary of a 10th-century lady-in-waiting. Nagiko grows up, obsessed with books, papers, and writing on bodies, and her sexual odyssey (and the creation of her own Pillow Book) is a "parfait mélange" of classical Japanese, modern Chinese, and Western film images.

Hubert is a French policeman with very sharp methods. After being forced to take 2 months off by his boss, who doesn't share his view on working methods, he goes back to Japan, where he used to work 19 years ago, to settle the probate of his girlfriend who left him shortly after marriage without a trace. There he mets his former colleague Momo and his daughter Yumi who he did not know was ever born. Hubert eventually finds out why his girlfriend left him and the reason becomes his and his new...