In ancient Japan, Kubo is an eyepatch-wearing young man who lives with his evil mother Sariatu in a give in on a mountain which is alongside a town. Consistently, he recounts stories to the town's local people including Hosato, Hashi and Kameyo by mysteriously manipulating origami that moves under music played from Kubo's shamisen. He tells the story of a samurai warrior named Hanzo who is Kubo's missing father.

At the point when the town ringer tolls flagging dusk, Kubo comes back to his mom as she expressly cautions him to not remain outside after dull or her Sisters and his granddad the Moon King will come to take his outstanding eye after they took his left one when he was an infant. One day, Kubo learns of a Bon festival which has a function where relatives speak with expired friends and family. He touches base at a burial ground and tries to address Hanzo, however leaves in outrage when his dad does not react. As Kubo remains out after dusk, Sariatu's Sisters Karasu and Washi discover him and assault.

His mom touches base to fight them off. She sends Kubo away utilizing her enchantment, instructing him to discover his dad's enchantment protective layer. He takes a bolt of her hair before she charges at her Sisters. Kubo awakens and meets Monkey, his little wooden snow monkey charm that was enlivened by his mom's enchantment. She advises him that his mom is dead, his town is crushed, and they should proceed onward to survive. The following morning Monkey wakes Kubo and calls attention to 'Little Hanzo'–one of Kubo's origami intended to resemble his father–who collapsed himself and woke up during the evening.

Little Hanzo indicates Kubo and Monkey the best approach to bits of an enchantment protective layer, where they are welcomed by Beetle, an amnesiac samurai who was reviled to appear as a stag scarab/human half and half and cases to have been Hanzo's disciple. He goes along with them on their journey when he discovers that Kubo is Hanzo's child. In the mean time, the Sisters find Kubo is searching for his dad's shield and split up to discover him.