A band of pirates called the Tinkerbats, led by Risky Boots, raids Scuttle Town and makes off with a prototype steam engine belonging to Mimic, the town's resident treasure hunter. Mimic warns Shantae, Scuttle Town's guardian, that if Risky also collects four magical "elemental stones," she could supercharge the engine into an unstoppable weapon. Determined to recover both the engine and the stones, Shantae sets out across Sequin Land to stop her.
With help from her friends Bolo and Sky and her acquaintance Rottytops, Shantae works through three dungeons and claims three stones. At a fourth dungeon she finds the last stone, only to be ambushed at the exit by Risky, who seizes all four. Using a magical flying telescope called the Sky Scope, Shantae locates Risky's hideout and teleports in, reaching and destroying the weaponized Tinker Tank. Risky tries to kill her but is defeated, and Shantae escapes the collapsing lair. She is then whisked to the Genie Realm, where the genies offer her a place among them as a reward for her courage — at the cost of never seeing her friends again. She declines and is returned to Scuttle Town, telling Mimic she had to destroy the steam engine, only to be reassured that it was probably for the best.