A young woman, adorned with a pack featuring a beetle emblem, embarks on a small boat across tumultuous seas. A boy's voice warns the observer to remain attentive, for what follows is a tale that must not be missed. Suddenly, a massive wave looms before her, but with a deft strum of her shamisen, she magically parts the water, allowing her passage. Yet, just as land comes into view, a rogue wave engulfs her vessel, capsizing it. Striking her head against a submerged rock, she is washed ashore. Awakening to a cry from her pack, she tenderly comforts her child, Kubo, who is left with just one eye.
Fast forward a decade, and Kubo (Art Parkinson) and his mother, Sariatu (Charlize Theron), have made their home in a cave on the cliffs where they washed ashore. Kubo has taken on the role of caretaker for his mother, who exists in a state of semi-consciousness due to the injury sustained during that fateful day. Kubo wears a patch over his missing left eye and drapes himself in a robe made from the cloth that once wrapped him as a baby, a relic of his father. Each day, Kubo ventures into the nearby village, shamisen in hand, enchanting the locals with vivid tales of the heroic samurai Hanzo, using origami figures that spring to life. Hanzo embarks on a quest, wielding three magical artifacts: the Unbreakable Sword, the Impenetrable Breastplate, and the Invulnerable Helmet, to confront his arch-nemesis, the Moon King. However, as Kubo's story unfolds, the village bell rings, signaling the approach of night, forcing him to hurry home.
That evening, Sariatu recounts tales of Hanzo, Kubo's father, and how he sacrificed himself to protect Kubo from the nefarious Moon King, who is also Kubo's grandfather. Sariatu reveals that Hanzo was a warrior akin to Kubo—a daunting figure for their enemies. She cautions him never to wander past dark and to keep Mr. Monkey, his protective talisman, close by. The stakes are high; if Kubo forgets her warnings, his life will be in jeopardy from the relentless Sisters and the Moon King himself. Later that night, Kubo awakens to find his mother speaking in her sleep, causing his origami to flutter about. When he inquires about the fate of his eye, Sariatu stirs.
The next day, a buzz envelops the village during the Bon Festival, where lanterns are lit in memory of the dearly departed. Encouraged by his elderly friend Kameyo (Brenda Vaccaro), Kubo hopes to spark a connection with Hanzo by lighting his own lantern. A local man, Hosato (George Takei), shows his daughter how to honor her ancestors. However, when Kubo receives no reply from Hanzo, frustration swells within him, leading him to crush his paper lantern in anger. Distracted by the passage of time, Kubo realizes that the day has turned to night. An ominous mist blankets the scene, and Sariatu's twin sisters, embodied by Rooney Mara, emerge, compelling Kubo to join them. Kubo flees in panic, only to have his mother intervene. She invokes her magic, granting Kubo the ability to sprout wings as he escapes. In a heart-wrenching moment, Kubo clings to a strand of his mother’s hair before witnessing her engage the Sisters, ultimately disappearing in a mighty surge of energy.
He awakens in a desolate landscape, greeted by a macaque monkey who reveals the grim news of his mother's departure. The monkey, an incarnation of Monkey (Charlize Theron), urges Kubo to flee and find safety from the Sisters. They take refuge in a whale carcass, where they enjoy a stew made from its flesh. Monkey reveals that she was Kubo's charm, brought to life by Sariatu's remaining magic, and together, they must search for Hanzo's magical armor. This armor represents Kubo's only hope against the impending threat of the Moon King. As Kubo presents Monkey with his mother's hair, she skillfully transforms it into a bracelet, a token of memory—the most potent form of magic.
The following morning, Kubo and Monkey discover that an origami figure of Hanzo has come to life overnight, silently guiding their journey. Their adventure leads them to encounters fraught with danger and excitement. After a harrowing abduction by a giant beetle who turns out to be Beetle (Matthew McConaughey), Kubo learns that Beetle suffers from amnesia, yet believes he was a valiant warrior and Hanzo's apprentice, now cursed to exist as a beetle. As they bond over their shared goals, Beetle expresses his desire to join their quest, vowing to protect Kubo with unwavering commitment. Monkey, though initially hesitant, acknowledges Beetle's dexterity with a bow and reluctantly agrees to the union.
Their next challenge presents itself at the Hall of Bones, where they must obtain the Sword Unbreakable, guarded by a formidable skeleton. Realizing that only Kubo can pull the sword from the guardian’s head, the trio strategizes their attack. Following their victory, origami Hanzo leads them to the edge of Long Lake, where repartee between Monkey and Beetle ignites over Kubo's safety. Seizing the opportunity to showcase his abilities, Kubo fashions a magnificent ship from leaves to traverse the lake.
During their crossing, Beetle teaches Kubo the art of archery while Monkey skillfully slices their catch from the lake using the Sword Unbreakable. In a moment of camaraderie, Kubo rejoices in sharing a meal with his newfound allies—a first for him. However, the journey takes a turn when origami Hanzo indicates that the Breastplate Impenetrable lies beneath the lake's surface. Although Beetle volunteers to secure it, Kubo warns of the lurking creature that ensnares any wanderer with its enticing gaze.
As a storm brews, Kubo dives in after Beetle, fearing for his safety. Meanwhile, Monkey confronts one of Sariatu's sisters, clashing in a fierce struggle. Just as the battle reaches its peak, Kubo discovers the armor but becomes entranced by the Garden of Eyes. In a desperate act, Monkey defeats the Sister, exclaiming that her love for Hanzo strengthened her. Upon his return, Kubo realizes that the mighty monkey is indeed his mother reborn. They seek refuge in a cave where Sariatu, in her motherly instinct, shares her backstory—how she was born in the heavens and tasked with eliminating Hanzo, but through compassion and love, she found herself and bore Kubo.
The plot thickens as Kubo dreams of an elderly man playing shamisen—a vision passed to him from his father's spirit. This mysterious figure instructs Kubo to seek the Helmet Invulnerable in Hanzo's ancient fortress. Excited, Kubo and his companions set off on their final quest. Upon reaching the dilapidated fortress, they discover images depicting the armor’s locations but no helmet. Suddenly, the second Sister confronts them, revealing Beetle's true identity as Hanzo, only for him to be fatally wounded in a moment of reunion with his family.
As chaos ensues, Kubo harnesses the power of his shamisen in retaliation, unleashing a blast that eliminates the Sister. In the aftermath, Kubo is left alone to mourn his parents. Despite the heartbreak, the origami Hanzo gestures toward a painting of the Helmet, prompting Kubo to realize it's hidden as a bell in his village—an artifact ringing at dawn and dusk. With determination, Kubo creates a bracelet from his father's bow string and his mother’s hair, strumming his shamisen one last time to break the final string. Majestic wings emerge, allowing him to soar back to his village.
As Kubo arrives, he warns the townspeople of the impending arrival of the Moon King. He hastily retrieves the helmet, completing his armor, and confronts his grandfather. The Moon King (Ralph Fiennes) appears, identical to the elderly man from Kubo's dreams, offering a tempting bargain of eternal life together if Kubo surrenders his remaining eye. Defiant, Kubo rejects this proposition, triggering a vicious attack from the Moon King, who transforms into a colossal fish-like monster.
Kubo finds himself cornered in a graveyard filled with his ancestors’ spirits. Harnessing his mother's hair, his father's bow string, and a strand from his own head, he restrings his shamisen while the Moon King ridicules him. With renewed energy, Kubo summons the spirits of his ancestors, conveying that their memories and love are the truest magic. As the Moon King lunges to end the struggle, the spirits rise, overpowering him and stripping him of his otherworldly strength.
Defeated, the Moon King becomes a mere mortal, left blind in one eye and bereft of memories. The villagers step forward, welcoming Kubo as his grandson, and each offers a memory of kindness to restore the fallen ruler's humanity. Courageously, Kubo steps up to become his grandfather's storyteller. As dawn breaks, Kubo lights two lanterns for his parents, expressing a heartfelt wish for their presence. The film culminates with Kubo setting the lanterns adrift in a flowing river, with the glowing spirits of his parents standing proudly by his side, a poignant end to his incredible adventure.
