The film is built on several heartbreaking and emotional twists. The first major reveal is that Monkey is actually the reincarnated spirit of Kubo's mother, Sariatu. She used the last of her magic before dying to transfer her soul into the wooden monkey charm to protect Kubo. Later, it is revealed that the amnesiac Beetle is actually Hanzo, Kubo's father, who had been cursed and transformed by the Moon King.
The ultimate tragedy of the film is that both parents are genuinely dead and cannot stay with Kubo; they sacrifice their reincarnated forms to ensure his survival. Furthermore, the film subverts the traditional 'hero's journey' trope: the magical armor Kubo spends the entire film collecting is ultimately useless against the Moon King's raw power. Instead, Kubo's true weapon is his shamisen, which he strings with the hair of his mother, the bowstring of his father, and a strand of his own hair. This symbolizes that love, memory, and family are the true armor against darkness. He defeats his grandfather not by killing him, but by stripping away his divine, hateful power, leaving him as a mortal with no memories, allowing the village to rewrite his story with compassion.