In ancient Japan, a one-eyed young boy named Kubo cares for his sickly mother in a seaside village. Kubo is a storyteller who magically manipulates origami with music from his shamisen, a traditional three-stringed instrument. His mother warns him to return home before dusk to avoid the vengeful spirits of his ancestors, particularly his grandfather, the Moon King, who wishes to take Kubo's other eye. During the village's Obon festival, Kubo stays out after dark, unintentionally summoning spirits from his past. His mother uses the last of her magic to send Kubo away to seek his father's magical armor, which is said to be the only thing capable of protecting him.

Joined by his protectors, Monkey and Beetle, Kubo embarks on an adventurous quest to find the three pieces of his father’s armor: the Sword Unbreakable, the Breastplate Impenetrable, and the Helmet Invulnerable. As they journey through the treacherous landscapes facing monsters and spirits, Kubo learns of his family’s history and the strength of his magical powers. Their path is fraught with challenges that test their courage, intelligence, and bonds of trust, while his vengeful aunts, the twin Sisters, and the omnipotent Moon King loom ever-nearer, intent on stopping Kubo and fulfilling the ancient vendetta.