In feudal Japan, 12-year-old eyepatched Kubo tends to his ill mother Sariatu (who bears a scar over her left eye as the result of a sailing accident at the beginning of the film) in a mountain cave near a small village. He earns their living by magically manipulating origami with music from his shamisen for the townsfolk, telling the tale of his deceased father Hanzo, a samurai warrior. Kubo is never able to finish his story, as he does not know how Hanzo died and his mother herself cannot recall the ending due to her mental state deteriorating. Sariatu warns him not to stay out after dark as her Sisters, Karasu and Washi, and his estranged grandfather, the Moon King (who took Kubo's eye when he was a baby) will find him and take his remaining eye.