Shantae, the half-genie guardian of Sequin Land, has been adjusting to ordinary life since losing her magical powers. Her uneasy peace shatters when the greedy Ammo Baron seizes control of her hometown and, moments later, her old rival, the pirate Risky Boots, turns up demanding to know who stole her crew and equipment. Together they discover a spreading Dark Magic tied to the Pirate Master, a fearsome tyrant and Risky's former captain long ago sealed away, who now schemes to return. Setting aside their rivalry, Shantae and Risky form a reluctant alliance and set sail across a chain of islands to stop his revival.